Undoutedly, my vote goes to Shuyin. You can say all you want about Seymour being a pussy, Shuyin is the worst, most annoying, fag in all existence! His story and reasons for destroying the word sucked. His voice sucked. He was a shitty boss.
I refuse to play FF10-2. Considering how "Charlie's Angels" the game looks to me, I'm genuinely not surprised to hear that the villain is a colon commander.
That said, Seymour was my least favorite villain in the series. Lame hair, lame voice, lame everything.
ExDeath from FF5. He had no story behind his motives at all. He was just some wanker demon that had been sealed away for trying to destroy the world before (again, for no real reason)