The vast majority of differences come down to simply matters of opinion. I prefer virtually everything about VII, but that's just me.

What sets Sephiroth apart as a villain, I think, is the fact that he actually had a purpose - to become a 'God', and to help his mother to recover her lost strength. Kefka, however, just like so many other FF villains, wanted to destroy everything - all life, even himself. Nihilism gets a bit dull, especially when there's so much of it.