Sounds fantastic, I can't wait for it to come out!

I love that you're adding Manichaeism into the game. The religious struggles are one of the most interesting parts of the late empire and should be a big part of the game. My suggestion would be to create "hidden" religious traits. For instance, a character might be openly christian, but have a hidden trait of being a pagan that might come out later in the game. I think this would create an interesting dynamic and add to the religious tension. I would also slow down the conversion rates for religious buildings to demonstrate the difficulty of converting a population