The villains goal and personality traits make him unaware of how bad or evil he is. He believes everything he is doing is for the good of man. His point of view is that he is the protagonist, and anyone who doesn't go along with him is a kind of antagonist (the main one being the guy who comes out of the control he's been under).
Most of the story will be told through the good guys account of events, bar a few flash back scenes. However the story will be split amoungst the two, making them both the heroes (in a sense) of their tales.
I'm now going to try and add the heroes goals in as advised. Thanks for all advice and comments so far.