Hmm, I'd have no problem fragmenting my pantheon into multiple churches, though due to in-game mechanics that's more of a handicap than a gameplay strategy. If a re-write was ever made allowing branches/chapters within a religion or group of religions (Sort of like diplomacy for religion I guess), then that'd be one thing. The current system rewards clumping of power... Perhaps if new mechanics were added, giving individual benefits for BOTH a build-up of numbers/followers/powers AND a more nomadic/loose/isolated religion system, since realistically each has their ups and downs, then it would make the religious systems much more interesting.
In the end, it mostly boils down to having the time, patience, and skill to make a religion and run it without getting bored or frustrated. Hence why I'm going to become a Priest when I get a chance, have a little fun on the side.
