Villains: I thought they were good. I don't want to get into the details of it as I will spoil the game for you, but for me, the villains all believed they were doing the right thing. Which is quite invigorating, instead of the usual: I'm an evil person and I want power. So I would say that is similar to Vayne in XII.
(SPOILER) And finding out that Cocoon was basically a chicken battery reminded me of the Matrix scene when Neo finds out that humans were being used as batteries. There are quite a few Matrix similarities I think