Heres my take. Jenova wants to destroy the planet, Sephiroth wants to become a god. While Sephiroth wouldn't want that originally, Jenova had manipulated him. However it is possible his will prevailed, however was still partailly under Jenova's influence, making them a Joint being with Sephiroth in more controll then Jenova. Since Jenova and Sephiroth would become one, Sephiroth becoming a God would indead make Jenova a God and destroy the planet in turn, being able to use the planets corpse and travel the Galaxy. That conclusion fits in with both the ambitions of Sephiroth and Jenova, but Sephiroth having more control would make him the head villian. Thats my take on the story, and No, I'm not a Seph fan boy, Im a Kuja and Kefka fanboy.