Red, for pretty simple reasons actually. I don;t want to get in a circular debate about the logic problems and plot holes of the different endings so to keep it simple:
1. I have no reason to trust the Catalyst, given his actions I would rather see him and his giant death machines out buisness permanantly. I don't want them walking around, I don't want to use them, I want them destroyed. I have no idea if they are going to one day turn and start killing everyone. Consider it destroying weapons of mass destruction.
2. I think the Catalyst is an idiot and I refuse to take any advice from a little monster, forced advice at that. Advice at gun point so to speak. I don;t trust the other endings, generally being granted all the power or being given a push button utopia have come with a very dangerous price tag. The little monster created a cycle, created a problem, and then came up with the worst possible solution to a problem anyone could have come up with. His Solution to a problem he caused. No thank you
3. Third and final, I want revenge, I want a reckoning, I want to settle accounts. The Catalyst ran up a hefty debt of blood for countless cycles, and he is going to pay what he owes. His list of crimes reads like a demons resume. I may not be able to save everyone with the red ending, but you can be damn sure i'll avenge them.
That's right I ripped off the Avengers, cause it's freaking awesome. If Udson can rip off Deus X, I can rip off the Avengers.