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To title this article a "defense" is actually a bit of a misnomer; it's more a ringing endorsement of the season.
I have rewatched most of the season, and have decided where S12 belongs in the pantheon of Supernatural seasons. 
  1. Season 5
  2. Season 2
  3. Seasons 1 & 3
  4. Season 12
  5. Season 4
My favorite will always be S5, with S2 hot on its heels. Then S1 and S3 are essentially tied, with S4 bringing up the rear among the Kripke seasons. I'm placing S12 just after S1 and 3 but ahead of S4, because this season was far more enjoyable for me than was S4 for reasons that I'll explain below.

Sam and Dean

Much of my love of this season derived from the brothers' relationship. Dabb promised that this year would have a S1 vibe, and that's just what we got between the brothers. This was the Sam and Dean I fell in love with in S1, and it has been a long time since we have seen them so at ease with each other, bickering and laughing and teasing, and ALWAYS having each other's back. The affection and trust between them was a joy to watch. I believe it is the first season ever in which neither brother was afflicted with a supernatural influence, and the first season since S7 in which we were not subjected to a lengthy, contrived conflict that was often based on out-of-character actions by one or both brothers.  It is true that conflict makes for good storytelling - up to a point - but lately the show has gone so far beyond that point that it was often devoid of the emotional satisfaction that is the sine qua non for my enjoyment of the show.  This year, however, we were treated to episode after episode of the brothers actually enjoying each other's company.  From lolling around on Jody's couch while Sam teased Dean about his hobbies, to their humorous conversations after Dean killed Hitler, to the way Sam anticipated what Dean needed after his night out in "Regarding Dean", to their bemusement over the fact that they were celebrities in the eyes of other hunters- I ended almost every episode smiling in satisfaction at their relationship. Sure, there were a few brotherly spats, of the type that has characterized their sibling relationship from the first season. But mostly, we saw a harmonious relationship between equals, a relationship in which they seemed so in tune with each other that they worked together on cases almost seamlessly, with a shorthand between them.
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This harmony resulted from the fact that, beginning in S11, Dean for the most part stopped treating Sam as a kid brother and began treating him like an equal partner.  He trusts him, respects his opinions, and often defers to him.  This was exemplified by his reaction to Sam's speech in "Who We Are." He looked by turns awed, proud, and affectionate as he observed how Sam commanded the room and assumed a leadership position among the hunters.  It was not that Sam has never led before, because he has, as far back as the very first season. But since S4 we have often been presented with a Dean who wanted to dictate many aspects of their relationship, and a Sam who all too often permitted it, because the events of S4 had badly shaken his confidence in his own judgment.  Under Carver, this situation worsened.  The brothers' relationship was contorted into one based on accusations, blame, and anger, in which Sam was constantly reminded of his perceived failings.  Little wonder that he has resisted assuming the leadership role that he had once adopted so naturally.  But as Dean began to suffer grave self-doubts after taking on the Mark of Cain (MOC) and then having an almost irresistible connection to Amara, he began to look to Sam for guidance.  He followed Sam's lead in S11 in focusing on the “saving people” part of the bumper sticker, and this season he deferred to Sam's judgment on working with the British Men of Letters (BMOL) and giving Mary space.  But as is typical of Dean, he never gave voice to this belief in Sam; that is, not until the wonderful moment when, as Sam was about to depart for the BMOL base, Dean told him “you got this.”  Maybe Sam didn't need to hear that from Dean, but I did.  Dean never doubted that Sam would succeed, reciprocating the faith that Sam has always had in his brother.
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This brings me to perhaps the primary reason that I absolutely loved S 12- Sam has finally and fully been restored to the status of a co-equal character with Dean. This had seemed to be the case at the beginning of S 11, in which we finally began getting a fair amount of Sam point-ov-view (POV) again after a 3-year drought.  Sam had a story line AND POV during the first half of S 11, and I could hardly believe it.  But my happiness came crashing down when his story proved merely to be a vehicle to begin the Casifer story, and we never heard a single word about it again.  He had minimal significance in the rest of the Amara storyline, never even meeting her, and he once again receded into the background at the end of the season.  Honestly, I was crushed.
As always, I started off the new season hoping for the best, and for once my hopes were rewarded. The show has finally once again struck a nice balance between the brothers in the story lines and episodes. Both brothers were intimately involved in each of the season arcs.  They each interacted with Mary both in a group and individually, and we knew precisely how each felt about her return, her departure from the bunker, and her alliance with the BMOL.  I would have been completely satisfied had Sam had just a couple of more sentences with Mary in "Who We Are," but at least there was no doubt about how he felt towards Mary, and we didn't have to infer it from Jared's facial expressions alone. So I was 99% satisfied with how it was handled. Similarly, both brothers had a great deal of meaningful involvement in the BMOL plot.  Indeed, "The Raid" provided them both with separate but excellent interactions with the BMOL which also gave each J (especially Jensen) some needed time off from filming.  That same balance was struck in "Who We Are," and it paid off huge dividends in what was one of my two favorite episodes of the year.  Finally, they both were involved in the hunt for Lucifer, his eventual capture, and the mission to track down his nephilim. This culminated in the amazing finale in which the brothers played equally significant roles. 
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This season we also received copious amounts of Sam POV, he was interacting with other characters as we haven't seen in years- Magda and her mom, Ellie, Lily, Mary, Rowena, and many others- and he was meaningfully involved in almost every episode.  He killed the alpha vamp, a hell hound, and a god, and he saved Dean a number of times, rather than always needing to be rescued himself. The focus switched back and forth between the brothers over the course of the episodes and the course of the season, instead of Sam routinely exiting the scene for no compelling reason while the script and the camera stayed with Dean. Sam has been shown to be the very smart, tough, competent hunter, as well as the sensitive puppy dog eyed Sam that we first met in S1, but whom we saw scant evidence of under Carver.  Even in the few scenes of a tied-up Sam, he was portrayed not as a damsel in distress, but as tough, smart and determined.  He never broke when tortured by Toni, and I loved his repeated “screw yous” as well as his taunt to her that he had “been tortured by the devil himself” so he didn't fear an “accent in a pants suit.”Although it was a temporary victory because he was unwilling to kill Toni, he managed to outwit her and almost escape. When tied up in "American Nightmare", he continued to use his considerable persuasive powers to dissuade Magda from killing Gail. There was not a single moment of Damsel Sam this season, for which I am eternally grateful.
Because I am first and foremost a fan of the brothers together, I was also happy that Dean too was treated well in this season's scripts.  He seemed much like S1 Dean, albeit older, wiser, and more mature, befitting a man in his late thirties.  He treated Sam with respect and affection, and even admitted to mistakes the way he used to under Kripke, but virtually never did under Carver. When he calmly agreed that Sam was right about needing to give Mary space, and right to want to at least try working with the BMOL, I was both astounded and thrilled. Formerly, Sam's decisions would have occasioned an angry outburst, extended coldness, and repeated reminders of how wrong he was. But not anymore.  I loved Dean this year, every teasing, laughing, fighting, fierce, moment of him. He showed his smarts in quite a few episodes, kicked ass in many others, actually killed Hitler (!) and finally used the grenade launcher (YAY!).  He also moved me beyond words when he succeeded in reaching Mary in "Who We Are".  This was the Dean who captured my affection years ago.
A common complaint about this season is that we didn't see enough of the brothers, and I can't disagree with that.  It is my primary issue with the season, but I have consciously decided not to be bothered by it anymore, because it is the new normal.  My preference would be a return to the days of all brothers, all the time, and no other regular characters, which of course will never happen. This year presented even greater difficulty than usual in juggling the need to have substantial brother time with the Js' need for time off. Dabb knew even before they started writing that Jensen would be having twins, and shortly into the writing process they learned that Jared too would have a new addition to his family.  The only way to keep the Js happy and give them more time off was to either separate them in the episodes (which I prefer that they do sparingly) or else to give more screen time to the other characters.  In the past, that second option rarely worked out because the secondary plots, including the storylines for Cas and Crowley, were terrible by and large. They were boring and often nonsensical (see S9, 10, and 11), which only highlighted the absence of the brothers.  
This year, however, the show had new and interesting characters to take some of the weight off of the Js. I enjoyed Mary, Ketch, and Mick so much that I found their scenes almost as engrossing as the brother scenes- but not quite. :) How many interesting new characters were introduced over the last few seasons? I can think of only one- Metatron. I loved Abaddon, but she was just a one-dimensional big bad.  The other new characters included Rowena (who was simply dreadful in the beginning) Clair (nuff said) and Cain, who appeared in but two episodes.  This season the cast of new and interesting characters seemed like an embarrassment of riches to me but we also had better roles for recurring characters.  I loved Lucifer in all of his guises, I enjoyed Jody more than I have in a few years, I liked Rowena more than I ever have, and I was very entertained by the Cas and Crowley buddy comedy at the beginning of the season. Both Cas and Crowley had some excellent episodes which allowed them to shine, such as "The Future" and "Stuck in the Middle", although as usual it became clear that the show wasn't quite sure what to do with them.  Bottom line, if it ever reaches the point at which the lack of brother time becomes so pronounced that I feel like the show doesn't revolve around them, I would be very unhappy, but this season was nowhere near that point. In fact, once the news of the babies came out, I was expecting there to be far more brother-lite episodes than there were. 
While I understood and agreed with the complaints about lack of brother time, I was mystified by the criticism that the brothers' relationship was lacking in emotion. This truly confounded me, mostly because I don't understand what comparison is being made. Up until S11, the Carver years were a terrible slog through countless episodes of discord between the brothers. Sure, there was emotion, but it was almost all negative emotion. For half of both S8 and 9, the brothers seemed to barely like each other, and their anger at each other seemed to simmer under almost every interaction between them. Instead of love and support, we got sniping, accusations, and outright hostility. At the end of many episodes, I was somewhat depressed. This was most certainly not what I looked for in the show; in fact, it was the very opposite of what had drawn me to the show.  It is the reason why S4 is my least favorite Kripke season. It was wonderfully plotted (with some exceptions) and there were quite a few outstanding episodes, but after a wonderful hug in the first episode, we barely saw another indication of warmth and affection between the brothers. That season culminated in Dean calling Sam a monster and Sam brutally beating Dean almost to death. Good times! While I admired much about the season, I actually found it painful to watch.  
That's the way I felt through most of Carver's years. Other than the end of S8, which featured the most bro hugs ever and a couple of wonderful scenes between them, there was little to applaud in terms of the relationship between Sam and Dean.  I honestly though Carver did incalculable damage to the brothers' bond, culminating in Dean's awful declaration in S10 that he wished it were Sam on the funeral pyre instead of Charlie, followed shortly thereafter by his attempt to kill Sam. Yep, there was lots of emotion between the brothers, but of the most unpleasant kind.  Other than in "Brother's Keeper", was there even a hug during S10 or S9? If there was, it is buried in my memory under the morass of unpleasantness that constituted much of their relationship. This depressing situation was largely rectified in S11, in which the brothers' relationship finally began to bear some resemblance to the one that gives me so much joy.  But there were no hugs until the finale, and sometimes their relationship seemed muted because Dean was mostly distracted and disturbed by his connection to Amara.  The only standout emotional scenes between the brothers  were in "Red Meat", a truly wonderful depiction of the strength of the bond between them.  There were some nice conversations between them in the beginning of "Baby" and in a few other episodes, but no more than we've seen in S12. And there was far less of the ease and lightness between them that S12 provided in spades.  
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We also were treated to some wonderful and quietly emotional scenes between the brothers this season, such as almost the entirety of "Regarding Dean"; the terrific scene at the end of "The Memory Remains", in which they quietly discussed their legacy and carved their names in the table; and of course the several outstanding and very moving scenes between them in "Who We Are".  We were shown angry big brother Dean threatening Toni in Episode 1, we saw Sam rush to help Dean up after he was flung by Lucifer in "Rock Never Dies", we saw Dean helping Sam up after saving him in "Stuck in the Middle". The only glaring missed opportunity for a broment was in "Mamma Mia". Sam's rescue cried out for an emotional reunion between the brothers, but such scenes are not the duo's strong suit.  We got a wonderfully written emotional scene between Sam and Mary, but I would have liked a conversation or hug between Sam and Dean as well. But while I would have liked more hugs between the brothers, the reality is that other than in S8, we have only rarely been treated to more than one in a season. More importantly, while hugs are highly satisfying, the quieter moments of love between the brothers can be just as powerful, and S12 was not lacking in such moments.  There were more than enough to keep this fangirl very happy.

The Season Arcs

This season was the most tightly-plotted since S5, with careful and continual attention paid to each of the three primary storylines throughout the season. All three storylines - Mary's return, the BMOL, and Lucifer - were introduced in the first episode, and while certain of them dominated different episodes or different parts of the season, none of them was ever forgotten for long stretches, abruptly truncated, or dragged out glacially and boringly throughout the entire season. There was almost constant movement on all three plots throughout the season, made easier by the fact that there was a great deal of overlap in the stories, all of which made sense from a story telling perspective. The Mary and BMOL plots intersected for much of the season, in a way that propelled both stories forward in a coherent and engrossing way.  The Lucifer story also became intertwined with the BMOL, first when the brothers utilized the magical egg to exorcise Lucifer, and then more significantly when the BMOL set their sights on the nephilim for elimination.  The intersection of the two storylines also included the nice surprise that Crowley had been working with the BMOL for many years, and that they were fully aware of his role in Lucifer's release.  Mary's story ultimately collided violently with that of Lucifer when she thrust him back in the AU, only to be trapped there with him herself.  I think Dabb did a better job juggling multiple storylines than any show runner since Kripke, who was a master at it.  Sera Gamble's seasons were uneven in this regard, although still light years better than Carver's.
Jeremy Carver is a wonderful writer, but his plotting of the seasons' arcs was atrocious. Without rehashing his tenure as show runner and all of its failings,  I will point out his plotting missteps that contrast so sharply with the painstaking way that Dabb developed the S12 stories and wove them together throughout the season. S8 seemed very much like two completely different seasons, the first of which was an awful, painful mess, and the second of which finally developed a coherent plot in the Trials, and in which Carver finally realized that the viewers actually prefer when the brothers don't seem to actively dislike each other.  S9 similarly abruptly changed its focus midway, from Abaddon as a big bad, to Metatron (and in the eyes of some viewers, Sam) as the big bad.  Carver belatedly realized towards the end of the season that he had left Abaddon off somewhere apparently getting her hair and nails done (she always was the most wonderfully stylish demon), so he abruptly brought her back so that he could kill her off in a laughable fashion, ending the plot that he had apparently lost interest in.  After dispatching the Demon Dean storyline in a blink-and-you-missed-it three episodes,  S10 focused for its entirety on one storyline, the MOC.  Unfortunately, NOTHING HAPPENED for vast stretches in the middle of the season. Hands down, it was the most boring storyline ever. I can sum it up in two lines of dialogue: Dean:  “I'll try to fight for as long as I can” (accompanied by much arm-rubbing and staring in the mirror); Sam:  “You can do this Dean, we'll find a cure,” after which he resumed standing silently in the corner like a tall, gorgeous lamp post. 
The first half of S11 indicated that Carver had finally righted the ship, because there were two decent storylines, one for each brother, which slowly unfolded during the first half. I was not particularly impressed with how the Amara's story unfolded, but at least we saw it develop and were treated to ongoing revelations about Amara and her effect on Dean.  Sam's faith arc was very nicely handled after its wonderful introduction in episode 11.2, right up until it became clear that ultimately it was intended to do nothing more than set up Cas's plotline as Lucifer's vessel. What a crushing disappointment to learn that Sam's journey of faith was ultimately meaningless, forgotten by him (ie, the writers) as though it had never happened. And Dean's quasi-romantic connection to Amara, misbegotten though it was, also culminated in no meaningful event. It was there....and then it wasn't.
But what a difference a year, and a change in showrunners, makes.  The first episode of S12 introduced us to Mary and the BMOL, and kicked off Lucifer's ongoing attempts to strike back at Chuck by causing destruction and mayhem whenever and wherever he could. In my eyes, these were all fresh and very engrossing storylines.  Mary's return and the introduction of the shadowy BMOL were both uncharted territory for the show, yet both had their roots in previously established canon. That is where Dabb and his phenomenal crew of mostly new writers excelled; they all remembered that the show had an actual history, that events and characters from previous seasons had an impact that reverberated and continued to affect the brothers' lives, and which the brothers naturally would reference at times. So we saw and heard references to events and characters from seasons as far back as S1, and this was long overdue. It has been so disappointing that the rich history and canon established in earlier seasons have been largely ignored the past few seasons, as though those events had happened in a vacuum.  
I also felt that Dabb and his writers were much more diligent about trying to be consistent with canon. Sure, there were some lapses, as there have been under every showrunner, but fewer than we've seen for many a season. We were even treated to explanations for some things that I had always wondered about, such as how and why did Crowley become the King Of Hell? Whatever happened to Crowley's son Gavin? Why has the alpha vamp never resurfaced? Who, if anyone, has the colt? What would a gathering of hunters be like?  And one of my favorites, what DOES happen to an angel when he's blasted away?  I absolutely loved the scene with the Casteroid.  It was exciting, unexpected, and hilarious to see Cas blasted through the sign for the Mystery Spot, only to land at the feet of baffled truck dude. To my mind, this scene from the first episode was emblematic of the season, which contained more excitement, surprises and humor than in many years. 
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The way Dabb introduced these blasts from the past was often masterful, especially the way some of them dovetailed in the same episode.  For example, "Stuck In The Middle (With You)" explained Crowley's ascension to the throne of hell as being due in part to his gift of the colt to Ramiel.  The colt then received its own excellent mini-arc, in which it was touched upon in all three season stories.  Mary stole it for the BMOL, who gave it to Sam to use against the alpha vamp, Eileen attempted to use it against Dagon, Sam used it against a minor god, and ultimately it was destroyed by Dagon when Dean tried to use it against her.   We also finally saw the grenade launcher used, after some tantalizing glimpses of it in Baby's trunk over the years. I loved the way the show teased us with a number of amusing references to it throughout the season, holding it in reserve until the penultimate episode when the brothers were most in need of it. It was a small thing, but one of the undeniable pleasures of the season. The three storylines featured intricate plotting which incorporated past events, as well as breaking new ground and bringing some wonderful surprises.
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 (Coming up in Part Two, a deeper examination of Lucifer, The British Men of Letters, Mary, Parent and Child, and Final Thoughts)