Although I enjoyed CoV, I agree with you completely. The games were virtually identical and you never really felt like a 'villain', more like a super powered errand boy in a dirtier city. It didn't help that you were often fighting the same people and doing the same missions as the heroes (except that instead of 'rescuing' someone you were 'kidnapping' them).

Personally I think that the only good way to have a superhero game with heros and villains is to have either direct or indirect PvP throughout the game, rather than in battleground type areas like the 'City of' games. Direct PvP is obvious, but by indirect I'm thinking more along the lines of things like WAR's public quests (you send your NPC henchman to rob a bank and a hero has a chance to stop you, etc).