Evil tree? LMAO.
Now that you mention Edea, I actually liked Adel and Ultimecia, Adel, cuz she was so freaking ugly and, just freaky, she didn't even look like a chick, and then Ultimecia was quite the oposite.
But these are far from my favorite bad guy: Sephiroth. Even though Jenova was behind him, he was the one you always fought against and the one you were always pursuing, and the one you fought the final battle against. Artist already described him well. I never played FF6 so I have no comment about Kefka.
Kuja, I hated that character deeply, I just hate GAY bad GUYS.
Seymour, I actually like him, I think the design is pretty cool, and he's a cynic motherf... but yeah, he's not that impressive either.
When I played FFX for the first time and saw Auron, I thought he was the bad guy, now, he WOULD BE A BAD ASS BAD GUY, although I prefer him the way he is