So, what types of powers/features would you like religions to have? They should be *active* powers. i.e. something that a player has to initiate to make it happen.
I was thinking you could use faith points (which would be gained regularly through peasant worship) which you can use for upgrades or one-shots, like in civ. Or do you have another mechanism in mind?
Some upgrades I thought of; a crusade upgrade that grants faith for hated religions killed in combat, a morale upgrade for units led by members of the church, etc. I guess these upgrades could require a one-time cost as well as upkeep in faith.
Some one-shots would be like spawning a unit of militia, giving a one-day bonus to combat against hated religions, instantly creating a new temple, etc.