I'm not trying to knock Kuja as being un-intelligent, I just don't think there is any discernible reason to consider him more intelligent than Kefka. I consider Kuja to be one of the better FF villains (costume design notwithstanding).

I always felt that how good a villain is can be measured by how much he adds to the game as a whole. And I feel Kefka added more to FF6 than Kuja added to FF9. Both are integral to the story (Kuja probably much more so) but whatever reasons you bring in terms of motivation/back story/intelligence it doesn't change the fact the I was always looking forward to any time Kefka was on screen. All of those elements are just and ends to a means.