I like the idea of giving religion a more important place in the game. For instance the possibility of denouncing a nation (as the pope sometimes did) which has negative consequences in regions where the population follows that faith.
And as far as I know churches already collect gold from peasants with temples etc.
What I would also like to see is the possibility of creating different 'factions/flows' within one religion, or even combining 2 religions which are similar. I mean, small churchess should be able to be stolen and converted to your own faith as well, or stuff like that.
But at the same time I also understand that this will prob take quite some dev time which may be better spend elsewhere.