I've only ever played the Woolsey version and I still think Kefka is a fantastic villain. Then again I also first played the game in 2001 and was still blown away by it, so make of that what you will.
For one brief, shining moment, I read 2001 as 1991 and charged up meh laser to deliver a scorching mockery you'd not soon forget, but then I actually read the post and now I'm disappointed.