Each civ's capital be the holy city of their national pagan religion at the discovery of mysticism (represented by their flag). for example: Germanic paganism, shrine is built for 75 hammers (supposed to be cheap). However, if a major religion comes along in the same city then the paganism is destroyed (exception is the shrine, which is destroyed by changing your state religion). national paganism spreads to all your newly conquered and founded cities, you may also buy inquisitors (10 hammers, again, cheap due to paganism's limited nature) to destroy major religions or enemy paganism (ex. roman paganism). Also in the civics screen you have two religious options available at mysticism: tolerance or persecution. persecution is basically a pagan theocracy minus the exp bonus. I would also like to see theocracy spread your state religion newly conquered or founded cities, and inquisitors unlocked at theology. Say, Spain is using theocracy and conquers Tenochtitlan, Spain's state religion spreads to Tenochtitlan. Inquisitors should not be allowed to destroy Holy Cities, and Holy cities (if founded on the same site) should be able to be rebuilt (how many times was Jerusalem rebuilt?). I think this is more of a mod thing than a patch, but it would be both historically accurate and add to religious conflicts. The only problem is that this seriously nerfs the creative trait and stonehenge (since everyone can build a cheap stonehenge for their pagan religion.) maybe combine creative and charismatic traits and make stonehenge give you really early calendar?