[Perndog]

FF6 wins because of Kefka. FFT had a better overall storyline, deeper gameplay (though I am partial to the standard Final Fantasy style), and more characters that were well-developed (no Terra or Locke though...). But FF6 had Kefka. Best game villain ever. He should have his own game. That cheesy synthesized laugh alone makes me misty from nostalgia.

EDIT: Oh, and aside from FFT's opening theme, all of the music in FF6 was better.