This is Hollywood. This is entertainment. There has to be a bad guy if there's going to be a good guy. It's that simple.
Is it? I just saw the Chan-wook Park movie Sympathy for Mr. Vengeance. It is a South Korean thriller movie. The main person are a deaf guy and his sister, who abducts a child who later dies in their custody. A lot of the movie is about the father, who seeks a very gruesome revenge. The main characters are certainly not good guys, and the way the father seeks revenge does not make him one either. This was very different from the good guy-bad guy-movies that I have seen from Hollywood, and is one of the few movies that have managed to stir up some strong feelings inside me while watching. All in all a very different movie (seen from a western perspective, I come from Norway). This is a movie, not a videogame, but I think the same could apply to a video game. The whole good guy-bad guy-thing should not be written in stone, and perhaps many game developers should think of new dynamics instead of having a very clearly defined good guy (often played by you) and clearly defined bad guys.
2.4 statute miles of surgical tubing at Yale U. = 1 I.V.League