Gatchaman Crowds Insight doesn't really have a villain.
You'd think the villain would be Gelsadra. He's the one who's ostensibly created the dystopian modern Japan, and he's responsible for the existence of the unity-craving Kuu-sama. But Gelsadra didn't really have to work that hard to bring all of that about, and doesn't seem particularly invested in maintaining any kind of power.