From Dust (2011) sounds like a very lite version of some of these ideas. The Raven Tower is a novel with a very similar plot including a war between gods who work through willpower rather than direct conflict. Receiver 2 has elements of the multiple layers of reality idea (and to a lesser extent, Anathem)
Similar to the sibling comment, I think the multiplayer recursive nature is what would set this game apart. The overarching theme being the exploration of the concept of fate, how much is within your control, and how much predestiny might play a role. And to be clear, I'm entirely non-religious, so there isn't a deeper agenda here.
