Can't at the moment really think of anything else.
But I'm also not sure if it's hard to mod. Just tested something right now:
- If you remove the "HolyCity" prereq from the shrines, a prophet will be able to build a shrine in every city, even if there's no religion. Since this does not really put the "holy city" in this city, a small python modification would be needed, but that's not a big thing.
- Problem: AI does not use it. I guess there are at this point not enough bonuses for the shrines. Adding some more (culture, happiness, whatever) would maybe make the AI use a prophet for it.
- Then the only other thing would be moving the tech prereqs for the religion founding to future tech, so that nobody gets them via a tech.
I'll maybe try that over christmas, if I don't forget it.