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Jenova was the baddest character because sephiroth was being controlled by his mother to do all the bad things he did, so since she was doing that she is the baddest bad guy.

Sephiroth all the way. Give credit to jenova for directing Sephiroth to the dark side but thats it

*Hits a buzzer and holds it down for a minute*

Sephiroth wouldn't even exist if Hojo hadn't created him. I'm not so sure it was ever Jenova pulling the strings...

well in my eyes i would say that they are both are bad.

*cough* If I may.....
Hojo had direct influence over Sephiroths birth and existance, but he was a mad scientist, so it wouldve happened no matter what. And Jenova pulled maybe one or two strings through Sephiroth, and that was only for a brief time. The time in which Sephiroth thought he was created in one of those test modules that made the Mako Monsters inside the Mako Reactor. During that time, Sephiroth lost all faith in his existance, and was coerced into finding the "truth" and had a plan imbedded in his mind for when he found out that "truth." After Sephiroth left the Shinra Mansion, he was back under his own control, utilizing the Jenova cells that were inside of him to their fullest. He regained his faith in his existance and had an even more enlightened view of himself, therefore shooting his willpower through the roof, taking control back from Jenova, who had control for so little time.
After ejecting himself into the lifestream (I believe in the Last Order view of things) he retained his control since he still would carry out his plan from this spot by utilizing the Jenova cells from a distance, since Jenovas will was weaker than that of Sephiroth, who had already been planted with yourn for Godhood.

*cough* Sephiroth was the better villain. And I hereby end my rant.

of course its got to be Sephiroth!

Well, if you go by that, then it was Jenova doing the tasks. Sephiroth made two present-game-time appearances in the entire game. That was in the Northern Crater when Cloud handed over the Black Materia, and at the end of the game.