@lizardsquid What are your feelings on the Xeno games, then? Particularly Xenoblade 1 and 2, since those are the ones we've (well, Felthry) personally played through.
@lizardsquid They're very very good games, with heavy religious overtones, but they tend to have themes of the religion not being the whole story, and sometimes being corrupt, and, well, I suppose I can't really say much more without being spoilery.
The Tales series has a few good entries along those lines too. We're fans of Tales of Symphonia.