This isn't for the best villian, it's for the most manipulative.

Sephiroth isn't even manipulative. He's not involved for half the game and it's Jenova that's doing any manipulating of the clones and whatnot.

From the poll, I'd have to go with Kuja, as he's behind the scenes for much of the game, truely manipulating what happens in the world of FFIX.