Cool, I think can see it now. I'd sum up the decision point as "how do you want this story to go?" (Is that fair?) If I decided to pray to Melora with my high Religion check, instead of using my okay-but-not-good Nature check, at that point I'm putting my PC's relationship with Melora into question, or at the very least bringing religion into the game. When I build my PC I'm going to invest in the resources that allow me to guide the fiction in the direction I want.
I guess one question is "why wouldn't you always use the skill with the highest modifier?" (Which makes me think of Burning Wheel's detailed list of skills.) That's probably a feature - the system reinforces your PC build choices by making whatever you're most interested in have the greatest weight so that you can reliably push the fiction in the way that you want, but on the same hand I can see how that would limit decisions because you'd always want to use that skill. The DM would need to be nimble, I think, to react and put pressure on the PCs and thereby the players.