I liked how on one level, XII's plot was much more simple and down-to-earth than the average JRPG plot-- not much more than two political factions squabbling over some magical MacGuffins and control over their little corner of the world. Of course, this is a Final Fantasy game so it has to go deeper than that, but they nicely avoided the typical plot twist where the leader of the opposing faction is revealed to be an unambiguously evil monster who wants to destroy all existence. Instead it's just another layer of political fighting, and it comes down to a question of which group comes out on top and which group continues to control or not control another group. It was messy, it wasn't just about good vanquishing evil, and maybe most intriguingly, it's the villains who end up succeeding in having their vision of the future become reality. Very FFT, except that you can actually comprehend what's happening.
Vaan may have been a bread sandwich but the other characters were likable and charismatic enough to make up for it. The English script was pure gold, best localization ever IMO, and the dub cast turned in uniformly excellent performances.
That's all to say nothing of the gameplay, which (again
in my opinion 
) just cannot be given enough praise. The Active Dimension battle system and the Gambits feel like a revelation. When I play it it feels like playing Super Mario Bros. or Gears of War and thinking, this sets a new standard for the way games are controlled, and everything before this is now obsolete. Of course, in this case the rest of the industry failed to get on the train and the ADB became a dead end rather than the new standard.
I guess it does live on to some extent in FF13's AI-controlled teammates and focus on party-level strategy rather than individual decisions. In any case I doubt very much we'll ever see another FF game with a vanilla, purely turn-based system, even if we don't see the ADB again.