I have heard rumors that there won`t be any religion in civ 5. But if these rumors were false, some changes I would have made to religion is:
One: A religion should be founded at a specific year. and in a random civilization. Chances could go up if you had the Spiritual trait or had priests or great prophets in your cities.
Second: there should be ways to get religion out of a city like crucifixion or exiling people of that religion. Then if you do this too much a neighboring citys or civilizations religious fanatics can attack you.
Third: If you have many religions in a city then riots may occur, because of religious confrontation.
What do you think? Sry for my grammar.