This was the idea I had a few months ago, in this here thread:
http://forum.paradoxplaza.com/forum/showthread.php?626701-My-idea-for-Pagans&highlight=
For those too lazy to click the link, the idea is basically that there should be a system that'll cause Christians (dunno about Muslims, probably not given their willingness to Holy War even each other) to not be able to jump straight to Holy Wars on Pagans. Instead, I thought that there should be a system in place where independent Pagan realms become an increasingly large blip on the radar of Christianity as they grow in strength, attack Christians, and resist the efforts of missionaries. So long as the realm is a smaller blip, the Christians will continue to resort to less war-like conversion approaches, and instead try to peacefully sway their neighboring heathen brothers to Christianity. If the Pagan realm, however, because too much trouble, then Christians will be able to declare your good ol' Holy Wars/Crusades to put an end to the growing heathen threat.
I think it'd create a more historically accurate depiction of the conversion of European pagans, and I think it'd make playing as a Pagan state much more enjoyable than their current state(indeed, I can't see their being much fun to being a Pagan if they leave the CB system the way it is, as it'll render some Pagans essentially unplayable thanks to the HRE and Russians). You'd have to walk a fine line between building power and not incurring the Wrath of Christ, and ultimately deciding whether to accept this new god as your own (and then try to push him on your likely unwilling vassals), or to hold onto the old ways and defy Christianity and history itself. Additionally, it seems like a more sophisticated, elegant idea to playable Pagans than "Give them more troops!" which is what most mods that make em' playable tend to offer as a solution.
I've brought it up a few times, and I know PI frequents these boards, so I really hope they at least took some inspiration from my idea. Cause, again, if they CB system between Christians and Pagans stay the same upon their release, its mostly going to be the same bloodbath, only now the player can experience the other side of it... and probably only continue playing if they play as gamey and aggressively as possible in many cases.