Out of the ones I've played? I'll probably get some flack for this, but Sephiroth. I like him as the First Class SOLDIER character that everyone idolizes, and would have even liked him as an antihero going to any lengths to stop Shinra once and for all, but I never cared for him all that much as a villain. He just felt too, "I'm crazy. Now I want power."

I might have said Kuja since he never felt intimidating or interesting at all, but I didn't play IX to the end so I didn't see him develop. Assuming he did... If he stayed the way he did at the start I'm changing my vote to Kuja.