Sephiroth without Jenova is actually better. Given Jenova's strength, power and wisdom, but lacking her control, Sephiroth is deadly.

Kuja could still win though. Not fast, but like I said, if he simply repels Sephiroth with powerful magic, he cannot be beat. Still, Sephiroth has a large chance of getting near Kuja and decapitating him. Kuja has Ultima and Flare Star, but Sephiroth appears to be able to fly and teleport. Using a destructive spell like one of thos very near his own person could result in a Double KO.

I'm backing Kuja, but I can argue myself all I like. That's not the point of this battle. Someone else post a good, lengthy battle plan for Sephiroth.

P.S. Don't call him a Genome. I doubt he likes being lumped in with mindless beings...thatt includes Zidane.