Now, personally, I liked the religion system and how it worked, but there are some things I thought would have been good ideas:
1): Religious downsides/ atheist benefits:
The only side effect to religion as of yet is diplomatic penalties, and these are relatively minor on Prince(Preferred difficulty as of yet) anyway. This seems very minor, as religious clashes have started wars and caused major prejudice. Maybe a few penalties towards passive spread to already-religious cities? The other thing might be to allow de-conversion in the sense that flaws in the religious principles or scientific development might create atheists from religious citizens, and maybe making it so that religion is optional, and atheist citizens from a certain technological threshold produce 2 instead?
2): / Incompatibility?
The thing I find a problem with is that science is technically evidence-based investigation and exploration, whilst faith is unjustified belief. Maybe an adjustable slider might help with this?
You can tell me your opinions. I might update the list occasionally.
You know it's interesting, I was just reading Davies' Eerie Silence about SETI and he articulated the connection between Christianity in the West and the rise of the Scientific Method. So I think there's some historical evidence to suggest that assuming faith cancels out reason is fallacious.