Under control of Jenova? Sephiroth was super-human due to the Jenova project, and when he found out his origin as an experiment it made him crazy which is why he destroyed Nibelheim and went on a rampage. Though his actions were a consequence of the Jenova project, he was still himself - the main protagonist to the story and it was the knowledge of the Cetra he gained from Jenova which led him to do what he did.
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Even then he didn't do anything all that villainous other than killing a flower girl
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What, you mean apart from wanting to absorb all of the planets energy in order to become a god?
How is he NOT the main villain? Just because his power came from Jenova, and his plan born from Jenova's knowledge does not make Jenova better, or more of a Villain. It was Sephiroth who carried out the evil acts, and Sephiroth who is the final boss. He looks kick ass, has kick ass music, is extremely powerful, has a gigantic sword and wants to be a god. That is why he is my favourite villain and why EGM voted him the #1 boss of all time and why he won the GameFAQ poll for best villain.
*Leaves Sephiroth fanboy mode*
