Games like Heavy Rain and Modern Warfare 2, to me, seem to get undue criticism of their stories. There are initial complaints about story that are invalid, and in fact have completely logical explanations. Then, delving further finds other issues; it takes some arguing back and forth before any such discussion reaches a point where I can only throw up my hands and say "You're right, that doesn't make much sense." But at that point it really doesn't matter, because that level of analysis is so far removed from what makes the game enjoyable that it doesn't affect the game itself. All games break lots of elements of realism, even in terms of people's motivations and how far they're willing to go, so I don't think it's unreasonable that Call of Duty brings about World War 3, and Heavy Rain has incompetent police officers (MANY real-life police stations have completely incompetent homicide squads!!!)
Anyway, Just Cause 2 has some pretty horrible reasoning in its story. In an effort to take out the violent, controlling government, you help some violent, controlling gangs to cause an uprising, and destroy government property that makes people's lives bearable, like bringing heat and electricity to their homes. Some games like Brink, Crackdown, and APB have you doing the exact opposite.