Frankly, I liked Kuja's design. It was very reminiscent of Kefka's rather androgynous appearance. And so what if Kuja went "good" at the end? Vader became "good" at the end of Return Of The Jedi, and he's the most badass villain ever. Kuja did things in the game that were ten times as evil as anything Sephiroth ever accomplished. I would much rather have a super-evil villain that goes soft at the very end, instead of a pretty lame villain that stays pretty lame the whole time.