FINAL FANTASY

[James]

Well, I still say Sephiroth was the main villain. There may have been higher powers at work, but he was the one you were dealing with the whole time. He fell into the Lifestream, and lay dormant in the Crater for 5 years. Doing so allowed him to amass power and knowledge from the planet.

Using this power, he was able to call Jenova and project a psychic manifestaion of himself (possibly, as it could have been Jenova). Doing so allowed him to lure Cloud and the gang to the Crater. He was the one doing it. If anything, Jenova was HIS puppet; serving her son.

And if you really want to nitpick, you could say Hojo was the main villain, based on your reasoning for saying Jenova was. But the fact remains that no matter who the most powerful person may be, you were still dealing with Sephiroth.

Besides, there is no FF game, to my knowledge, that doesn't have the main villain as the final boss.