I'm relatively divided between the two of them; I like them both a lot but for different reasons.

Kefka, I think is a more memorable villain. He has much more amusement value and I find that his evil is generally more unhinged and less logical. He appears a bit bumbling and soft when you see him in Doma and Narshe, and you're never quite sure whether to take him at face value. I didn't think he was the deepest villain ever, but he's presented well and is different from your typical villains.

Kuja, I probably marginally prefer, though I can't remember how I voted in the census. His reasons for what he does are more emotional than Kefka's and for that reason I think he's more evil in his motives, if not in his methods. Kefka's unhinged and that fact is made clear from the off, whereas Kuja hangs around in the shadows a bit, schemes and manipulates. The way Kuja knocks off Brahne was clearly something that had been in his mind for quite some time, whereas Kefka betraying Gestahl seems to be more primal and something he seizes when he sees it in front of him. The thought had clearly occurred to him before, but I see him as less conniving than Kuja, who clearly only became involved with Alexandria in the first place to further his own goals. The emotional level of villains is something I find to be relatively hit-and-miss, but I find Kuja to be believable, to have a bit more substance than usual and to just be generally quite cool. For all those that criticise Kuja for looking feminine or whatever, I think that's part of his charm - he's clearly not of this world, is mysterious and unique - it makes finding out more about Kuja that bit more interesting, whereas Kefka doesn't really have that.