Hm. Well, as of the full game's ending:
[spoiler]
It's still open-ended. Cygnus isn't Yahweh, as I thought originally. In fact, you can talk him down during the final battle by besting him in a theological debate. So he seems to honestly believe in Yahweh -- he isn't simply making it up for his own gain. But then, how is he a "prophet"? Where do his visions come from? Where did the vision after the bandit mission come from? He also uses very strange abilities when you fight him -- he is able to make copies of himself, create solid state shields, and even perform a mass teleportation. Now granted, we don't know the actual limitations of psychic powers in this setting, but that seems like something out of the ordinary to me. The fact that he has Mass Juxtapose, a spirit-based ability, also lends credence to his gaining powers by another source. Still, I do like the theory that the cultists are psys who don't realize they're psys -- they think their powers are divinely granted. But then, where did those high-level Scans that the Nameless One mentioned come from?! Agh...
The ending is just so unsatisfying!

I really hope we get a sequel, there are just too many things left open.
[/spoiler]