What I would suggest is make the main character's goals evil. And make his antagonists the good side. Also, this is just a personal view, but I think it would be really good if the game had politics in it, has in make that its main backdrop.
Has for the evil guys, make them diverse as possible. There aren't many good cliched evil guys except with a few exceptions. Also, give them a good reason for them to do what they are doing.