The three main antagonists of the game would probably be Queen Brahne, Garland and of course Kuja. Brahne was a woman tormented by the loss of her husband and who was then preyed upon by a devious mastermind, causing her to commit the terrible crimes she did. Garland was just a man created for the sole purpose of restoring his planet and people and he did that the only way he knew how. Kuja was a person who wanted to save his own life and show the proof of his existence.
So...are there any villains in the game who aren't sympathetic or deep? Who just want to destroy and kill and be all evil for no reason?