I agree with The Man to the extent that I originally endorsed the Jenova Control theory of Sephiroth. But even if that theory was not explicitly rejected by everything since then, it was horribly and inadequately developed in the game itself. Sephiroth had a lot of potential to be a multidimensional, sympathetic villain. But he didn't turn out that way, which I consider to be one of the many examples of lost opportunities by the FFVII writers.
Vayne was understandable and had more depth than your typical FF villain, but he wasn't very sympathetic. Kefka is not remotely sympathetic, despite being a great villain.