I'd say FF VI has the best characters, like many others here. For me, Sephiroth slightly upstages Kefka, I think, so it doesn't quite win for villains, but it still wins overall.
Final Fantasy VI switches perspectives so many times that by the end you really feel like you've taken part in a whole world, and not just one person's story. That feeling really epitomizes and strengthens what's great about the Final Fantasy games: The worlds that you explore are so unique, not just aesthetically and in their production values, but even in the one-liners the NPCs deliver over and over again, and in each world's myths and legends which define the struggle between good and evil.
Each main character's story in FF VI could stand on its own in a game full of goofy sidekicks, and would make a good game. When you put them all together you get the ultimate Final Fantasy, a story where by the end you feel like you're the world's life-force behind the scenes, rather than any one character, guiding a bunch of flawed warriors in a war to rebuild the world.
My runners-up are Suikoden V and FF IV.
