"Greatest villain" is far too vague. You can compare too many different areas, and then there are also the different worlds they are in. Would Kefka have dominated without his armies doing all of his work for him? Sephiroth seemingly did all his work on his own. Having said that, you could also argue that surely any true great villain will command an army, manipulating many men to do his bidding for him. Of course, then you could also compare pure strength - is Kefka more powerful? But power alone will never get you anywhere so long as you are able to be defeated - would Sephiroth be too quick, too deadly in his movements for Kefka? There is too much to debate to ever truly decide which would defeat the other in a fight. After all, if the player controls the characters in either game, they can lose the game and see a Game Over screen. They don't have to beat him. It would obviously be kind of silly, but you get the idea. Assuming they are defeated, however, do you also consider the manner in which they were defeated? Can they come back again of their own will, somehow? Is that truly defeat? Is that just a case of one set of playable characters being weaker than another?

Again, it's always going to be down to sheer opinion: Which villain do you prefer? If you're going for the overall greatest villain based on a personal opinion, does that opinon count? Do you prefer the opinion of many to the opinion of few? But what about percentage of those that have played and completed both games, which percentage prefer which? It's a toughy. So that's why I stick to personal opinion alone.

I like Sephiroth better because for me, I prefer an evil character that is capable of doing things on his own rather than using an army. I prefer an evil character to also be someone who I look at and go "Oh, he's pretty evil" rather than "What the hell is that?" Sephiroth fits those bills better than Kefka. Obviously. I like how Sephiroth doesn't run rampant destroying the world but rather does exactly what he personally desires - getting rid of the individuals he wishes to rid himself of for whatever reason, and only bothering with mass destruction of the world when it is done in a way that will not only benefit himself but also in a way that will wipe out everyone in a single blow. Impressive, I'd say.

These are my kind of reasons.