If you've never gotten into a religious war you are missing out. I've had some good times with Turin and Sigurd. Auto De Fe's religious takeovers, persecuting heretics, regions going crazy when your religion is declared evil. I do however notice this kind of fun seems to be the exception rather than the rule for religions.
The problem is it's hard to get people to participate in religions. Church of Aaron took around a year to get up to speed. Now I hear it's basically dead. It has members but no one talks or anything.
I think the devs should consider increasing the paganism penalty. Officially paganism is a collection of peasant superstitions that are supposed to be shameful for nobles to believe in. Unofficially however it's really no big deal. I've never once seen a noble mocked or called out for being a pagan. The fact is it's hard to get people to check their modern sensibilities at the door and act like medieval nobles. That's why we need game mechanics that incentivize it.
Right now being pagan is a very minor drawback for a region lord. In fact they'll suffer worse penalties if they choose the wrong religion. A pagan region lord should get a message along the lines of "The region's lower gentry are horrified that their new lord believes in peasant superstitions rather than following a proper noble faith" and the penalty should be a severe. It could be a penalty to realm stats, or perhaps gold production with further flavor text explaining that many nobles are refusing to pay taxes to a pagan lord. Mere knights can be pagans if it pleases them, but once you're a lord it's time to get serious.
The other thing preventing the sort of scenario PolarRaven wants is that religions are usually highly regional, sometimes even directly tied to a realm. When they're more spread out the religion is probably so tolerant that no one feels threatened by it. The reason a lot of religious strife has happened in the past is that tolerance and persecution varied over time. In the Roman empire for example the Christians were relatively unmolested under the Antonine and Severan dynasties, and throughout the crisis of the Third Century. They were even able to openly build temples. Then the persecutions of Diocletian came around and that really got the Christians riled up. As another example in the middle ages Christian regions might have varying levels of toleration for Muslims and Jews. These groups might build communities for a time only to be driven out soon after. The same is true for Christians and Jews in Muslim lands.
