This development diary from Paradox runs through the impact of religion in Europa Universalis IV. Given the game's intention to realistically simulate the empire expansion and strategy of the era, I'm sure it'll only be a tiny, insignificant part of the game. After all, when has a ruler ever corrupted religion for their own gain? *Checks Wikipedia* Oh... Oh, wow. Er, you should probably pay attention to this video.
"Will you allow reformation when it rears its head in Europe or stand your ground for Catholicism? Will you forego Christianity entirely and become a champion of the Muslim or Buddhist faiths?" My plan: largely ignore it. Not because of any strongly held beliefs, mind, but instead because I have faith in my own incompetence at balancing all of the game's systems.
Europa Universalis IV is due out this August.