I'd have to say Shinra. Every time I play that game, I legitimately hate them. They murder people and will wipe out entire towns just to prove a point. Their control extends over the entire world, and they oppress people. Not only have they taken over their homes, but they've taken their hope as well.

Even once you move past Shinra and onto Sephiroth, I'd still say that hatred towards Shinra doesn't let up. While Sephiroth is the one who's trying to summon Jenova and destroy the Earth NOW, it's not like Shinra every actually redeems themselves (except for Reeve).