1) I know it's probably pretty difficult to program but there's gotta be a way to make Cynical increase your Reason. Maybe make it so you can adopt an Atheist-specific trait that functions the same but also increases Reason.
2) Speaking of "religion"-specific traits, not believing in gods during such a violent time on earth would very likely mean very different things to different people. I propose four traits:
-Optimist: Increase in general opinion, health, and diplomacy
-Nihilist: Very high increase in intrigue and plot power, decrease in health and in damage against religious enemies
-Opportunist: Increase in martial, personal combat skill, cruel opinion, with a decrease in general opinion
-Scientist: High increase in learning and Reason gain, decrease in personal combat skill, moderate increase to damage against religious enemies.
These can be changed based on other traits the characters have and related events, and basically work like the Dharmic sub-religion traits.
3) Four of the five holy sites make sense to me, but I think Jerusalem should be replaced with Atheniai, mainly because, well--Jerusalem.
4) (Cheeky) Evil God Names: All of them.
5) You might want to keep the general functionality of churches but simply make them libraries/schools.

I've barely played the mod so if any of these are already in the works/in the mod, I apologize for my negligence.