My two wooden nickels:
If you look away from the story for a bit, you'll probably see that XII seems (to me, anyway) to take a decisive step away from previous FFs: Shiva, Ifrit and all those other summons-gang are revived as airships, later destroyed. New names for the Espers, all vicious-sounding. Battle-system much revised, quite a lot like ye olde Infinity-powered D&D-CRPGs some of us know and love. (Although with this battle-system and the graphics, FF12 felt more like what Summoner 2 should have been...)
Continuing along those lines, the story seems a fair deal more mature - and the dialogues are written in such a beautiful english! That alone can cause a replay! By mature, I simply mean that all that in-your-face drama FF usually brings with it is pretty much absent. No moral pointers, it lets things be as complicated as they indeed are. I love that aspect of the story no end, but that's me.
I agree that the Occuria/Venat gets quite little exposure, but I was unable to play the game "cover-to-cover" - for largely irrelevant reasons I was sometimes away from it for weeks on end. Maybe it'll clear up in another play-through.
As for Vayne being a villain or not, he always was the antagonist, anyway. To yet again spawn some D&D here, I'd say he was True Neutral rather than strictly speaking evil. (As I understand it, True Neutral means that the person in question will follow laws when it suits him/her, violate them otherwise [patricide? fratricide?], doesn't care much for good or evil if there's nothing to gain from it.) I could stretch myself to Neutral Evil if needed... but we all know the really vicious demons are fighting it out in the Blood War, determining whether Chaotic Evil or Lawful Evil is the worst.
... Maybe I should just shut up now. I bin playin Baldur's Gate 2. Yea.