A lot of great video games let you play the good guys. A few good games like Dungeon Keeper and Tie Fighter let you play as the bad guys. What I really want is more quality games that show both sides of the conflict. Not just in the sense of an abstract opposition faction with a re-skin of the same basic unit types, but rather a complete shift in priorities to reflect the cultural lens from which the world is viewed. Here's a trio of examples to illustrate what I mean.
The last suggestion might sound like a stretch since Nintendo isn't the kind of company that supports malicious gameplay...or are they? Don't forget about Wario. If he can get his own collection of games I don't see why Ganondorf can't get at least one storied adventure.