Well Kuja would not only win. He would annihilate Sephiroth and personally i dont see Sephiroth like evil.
He was FF7 villain yet i see him more like a misunderstood soldier that follow the path he beleive in.
For me he was just fighting for his own reason like any soldier he was loyal to his mother/master Jenova.
Sephiroth was nothing more then a puppet of Jenova.


Now let s talk about evil Kuja and Kefka destroying ppl wasnt enought they wanted to rule and bring the world to their knee.

Quality
Kuja : Beauty, Powerful, Genius
Kefka : Powerful, Genius, Crazy

Anyway why is evil born ?
Your just born whit it ?
Blind-Hatred toward something ?
An Impulsion that takeover when your in bad emotional state ?
Or just because you didnt get a hug when you needed it?