How about this
Each civilization starts with is own pagan religion which spreads to other cities in your empire when you found new cities however if one of the "researched" religions is introduced to a city then the pagan religion ceases to be practiced and the city adapts the new religion
You could also split Christanity into 3 seperate religions Catholic, Orthodox and Protestant and Islam into Sunni and Shiite
If we step outside the box abit we could introduce political idealogies as late "Religions" such as Fascism, Communism and "Western values" (Democracy, Civil rights etc)