The first thing I'd do is flesh out the internal conflict between Pagans and Christians within Pagan countries. This occurred a lot, after all. What would be absolutely wonderful would be for Christians to be able to send out missionaries to Pagan lands, causing some local rulers to convert and fight the Pagan "loyalists" for control. As a Pagan ruler, you could have the choice of tolerating them - with a risk of having some of your population or vassals convert, but with the benefit of improved relations with Christian neighbors - or banishing and killing them to preserve the ancestral faith. Heck, this could be modded into the "inquisition" job of court chaplains.
Even better would be if the degree of these missionaries' and converts' success strongly affected the moral authority of the respective religions, with high MA granting assorted bonuses - especially military - to Pagans. These were, after all, local religions of identity, and apart from fighting them with fire and sword, Christians also sought to undermine the various pagan state and tribal entities from within, often only achieving success once they were weakened and divided by the scattered conversions. This would make for a very interesting Pagan game indeed, with interesting strategic choices. The player could act like the Lithuanian Grand Dukes, uniting the tribes and then joining Christendom, act like the Prussians and fiercely cling to the old ways, finding military strength in religious zeal, or - as a minor county-level ruler - shrewdly convert, marry a Christian and use foreign help to betray and overthrow your ruler.
Unfortunately I'm horrible with scripting, at least as long as there's no scripting manual, so I can't offer much beyond concepts
Even better would be if the degree of these missionaries' and converts' success strongly affected the moral authority of the respective religions, with high MA granting assorted bonuses - especially military - to Pagans. These were, after all, local religions of identity, and apart from fighting them with fire and sword, Christians also sought to undermine the various pagan state and tribal entities from within, often only achieving success once they were weakened and divided by the scattered conversions. This would make for a very interesting Pagan game indeed, with interesting strategic choices. The player could act like the Lithuanian Grand Dukes, uniting the tribes and then joining Christendom, act like the Prussians and fiercely cling to the old ways, finding military strength in religious zeal, or - as a minor county-level ruler - shrewdly convert, marry a Christian and use foreign help to betray and overthrow your ruler.
Unfortunately I'm horrible with scripting, at least as long as there's no scripting manual, so I can't offer much beyond concepts