Prepare for a poorly formatted and incongruous post, as I'm way past my bedtime (I hope to edit this).
12 is by far the best in the series for me, while I recognize that Turn-based does have it's depth, it has always bothered me as a tedious and non-game aspects (this coming from a pretty big fan of platformers).
In the very beginning I was just entirely shocked by it's real-time combat and then the crazy targeting lines and flying enemies- yeah it's just screamed potential to me. I love it when a game finds ways of overwhelming you (another of those experiences I've had would be with the demo of Z.O.E.-gotta play that game). That's where I see some of it's failing points too of course. For example, I always loved the idea of summons/GFs/Espers, but through the entire playthrough I couldn't find I use for them(was I doing it wrong?). The idea of dual kingdoms really never broke through in the end, I thought it might be some amazing doubling of content (I really love long games, lol). The guy(throne-bearer, heir, chancellor) was just some 'cool' figurehead, with no real purpose, I guess maybe just to tell you you're one of the good guys.
Balthier's father, Cid, really didn't live up to his role in the game. A short (but very strong and cool, in the way he could use quickenings against you) boss and a little drama, but really one of the lesser judges in my eyes. Penelo was probably the most underdeveloped character in the game, but I really think Vaan just gets way too much hate, because of his weak sense of dress code. Yeah, it bothered me too, but I didn't refuse to play as him or anything.
While the simon-says nature of the quickenings bothered me at first, I really started to yearn for opportunities to use them, in part because I had my gambits figured out pretty quickly, so it broke up the doldrums of combat, plus it's high-score kind of nature (I think I got around the 40 range?). It was kind of strange how deep the nature of it felt. It was also nice that you could play it totally real-time or pause-break during harder battles too).
Another thing that bothered me, was although I beat the entire game without any sort of guide/help, is that I'm told it basically required a walkthrough. Apparently you couldn't get the very best weapon in the game unless you didn't break some innocent jar (among the thousands you did). I would be shocked if I were to find out there was some kind of in-game clue to something like that. There were a few other head-scratcher parts which I was never able to figure out, including a hunt and an Esper and blank spots (giving me the feeling I was missing something)... I hope to get back to those someday, but I'm not expecting much payout.
In terms of development, I think it was interesting in that while not every character had a giant monologue or endless inter-relations to plod through, they all had their own environment kind of dedicated to them. Basch had the prisons, and former judge life; Balthier had the skies and his freedom away from his father's position; Vaan had the underground and city-folk relations; Penelo had a nurturing sense and was attached to nature (much of the friendly wilderness was in her domain -- and Vaan of course); Fran had her race... which was a little messed up and confusing (much more than Vaan, I found a race of Victoria's Secret female bunnies disturbing), but her sixth sense attachment to the mist was a major payoff; Asche had the entire kingdom and all of it's holy relics to assert her responsibility for the land and it's people.
Grand_Arcana's comment has me very intrigued again as to what sort of premises were missed out on, and the connection to War of the Lions and Vagrant Story.
I guess you could say I can see what some people find in Final Fantasy 7 (which I haven't played), despite that game's combat not interesting me much.
In regards to end-game combat, yes it did get a bit dull, and it was kind of embarassing to just be guiding the characters around... but the character's really were still quite active, I guess you could just say there wasn't enough button-pressing, as tedious as that may get in associated titles. The biggest problems were:
1. Again, the Espers seemed useless.
2. 1000 needles really became the only active option, other than buffs/heals in most of the major fights. Playing it wrong? (I may have died at Cid... maybe once after that?)