This doesn't even get into the expansion, which I find odd. Sure there's aliens, but what about the Free Drones, or the Data Angels? It feels like there's a clear analogy to some of the discussion going on today (re: Google) where the morality of the DA might matter. Or, if you want to go environmentalist about it, the Pirates. The article talks about altering the sea levels, and there's a faction who actually prefers the ocean to land.
It is pretty telling to me what the devs thought that the Spartans canonically lose in their vendetta against the Gaians after the mind worms are controlled. And the Fundies can't catch up before that 10 year research prohibition bites them hard.