I have to agree with RPGillespie, because the question is far more complex then it seams. That said...
-- Spoiler Alert --
A literal comparison isn't fair. Kefka is human while Septh isn't. So, to be fair, the only real comparison that can be made was when they were at their peak villainous power.
Pt. 0 - Fan Clubs
Both had their own fan-clubs, where they would drudge around and say their name. (Ha, I just thought this was funny!)
Result - Evenly Matched
Pt. 1 - Allies
Kefka had his "bean-stalk of mutants" just like Septh (putting the story aside) had the Jevona-z. So, no real difference there.
Result - Evenly Matched
Pt. 2 - Cruelty
Kefka took perverse pleasure in other people's suffering. Septh just didn't care and simply wanted everybody gone.
Result - Kefka is -sick-.
Pt. 3 - Mental Stability
Kefka was a complete psyco, never calm, and had no real purpose outside of his own ego. Septh was also a psyco, but he was calm and had a specific purpose.
Result - Kefka had no purpose for his acts.
Pt. 4 - God-Like Power
Kefka has his Judgment of Light (i think) which acted more like a scalpel. It was very quick and annihilated anything in it's path. Septh had his Meteor spell, which was very obvious and slow. The only advantage was that it --would-- break up the planet.
Result - Kefka has the faster "your gonn’a die now" attack.
Pt. 5 - God-Like State
Kefka had retched a god-like state. Septh needed to destroy the planet before he could reach that level.
Result - Only Kefka had reached a God-Like state.
Physical Build?
When your a Demi-God, does this 'really' matter?
Battle Magic?
For differences in stats and such, I'm not bothering with this.
Well, I'm surprised! I thought it was an even match, perhaps I missed something? IMHO, Septh is a better character and obviously looks much cooler. But... Kefka is the better villain because he is "faster" and a "sick psycho".