The game strongly hints they are all on the same page about bringing back the Maker. That's partially why I hate the ending cause the conflict is far from over cause there are still the fal'Cie of Pulse to deal with, not to mention all the Deus Ex Machinas and red herrings the ending has to begin with.

I think its hard to argue that XIII dropped the ball with the villains in this one. The more interesting conflict in the story was the characters dealing with their destiny as opposed to a battling a well thought out villain.