I picked FFIV. Obviously.
I personally feel that the character development and storyline was really leagues beyond all the others in the series. What might be my favorite aspect of the game though was the variety of characters abilities and the fact that you always had a set party. Members would come and go, die, grow up, or transform and each encounter with the umpteen different parties provided a certain challenge.
I'm seriously tiring of having gigantic 10 character casts that allow you to switch whenever you want. It really takes you out of the game to think that you've got 3 enemies infront of you, and 7 party members just sleeping without helping at all. No support, just like they're dead. But as soon as the monsters are gone, they're all alive!