Really happy to see Asad quoted around here. Asad has written a number of things, but really the key point here is a bit what
@Sirimiri is saying - the practice of religion often is overlooked in favor of a focus on doctrine or belief. Asad studies Christianity, Islam, and secularism and tries to problematize the ways that categories of religion have been taken for granted (and secularism).
The issue here is this - with Asad, and with a lot of the other interesting and nuanced discussion about the line between religion and culture, "animism" and organized religion, we get really fascinating ways of looking and rethinking how we see religion.
But what to do about the game? This is a non-rhetorical question. There's many elements that one could think we could bring into a game - a papacy or other religious leader external to states, religious languages (e.g. Sanskrit, Latin, Old Slavonic), syncretism, animism, but at the end of the day these are going to get condensed into bonuses/maluses. In essence the problem is this: culture, religion, politics, etc., are clearly more nuanced than the kinds of categorizations that political scientists have made. But to put these things into a game, even one that, like the Paradox titles, seeks to be more of a simulation and less of a "game", is really difficult.
It's a challenge that I find really fascinating, and is part of the reason why I'm excited to be working for Firaxis, but it would be impossible to do in a way that would be faithful to the reality. I am reading these suggestions with great interest, though.