Sephiroth seemed like he wanted everyone dead in Kingdom Hearts and he wants to destroy the planet with Meteor as well as become a god. Does that not scream "I AM A VILLAIN MWAHAHAHA!" to you?

JENOVA wasn't the main villain because she DIDN'T DO ANYTHING EXCEPT USE SEPHIROTH.

Hojo isn't the main villain in THIS game because he has his own villanious spree in DoC.