OK, at the risk of repeating what others have said on this thread-this is what I HOPE religion will do for the game:
1) First of all religions, like governments, can change throughout history-according to when you 'discover' them.
2) Also like governments, each civ will have a range of most preferred to most detested religions. This will effect what religion your people demand you change to, and how readily they accept a religion you convert to.
3) Each type of religion will have its own range of pro's and con's-and it's own set of units and buildings. These buildings only have their full effect when you're in THAT religion! Culture and tourist effects remain, however.
4) Aside from the main religion types, you would also have the opportunity to introduce 'Orthodoxy' or 'Reformation' to your religion-again, each choice will have benefits and penalties.
5) Culture groups would effect how different nations, of the same 'Broad' religion-type, view each other. For instance, though A European Monotheistic' civ might 'despise' a European 'Polytheistic' civ, but would also look askance at a Middle Eastern 'Monotheistic' civ.
6) Definitely should have 'Religious' or more appropriately 'Cultural' Great Leaders, should definitely be part of the game. They could rush build cultural wonders, be sacrificed for a 20-turn culture boost or used to convert foreign cities to your 'cause'!
7) Heresy and religious conversion: If you neighbour a nation which has a different religion to yours, there should be a chance of one of your citizens 'converting' to their religion-and vice versa. The base chance is modified according to your cities population, if your city is connected to the other civ by a trade route, the relative culture values of your civs, the presence of other converts in that same city and how your people 'view' that religion (most preferred vs most hated!). These converts can, if there are enough of them, cause a 'religious' schism, whereby they break away to form their own civ-based on the new religion. They can also be a source of discontent and potential revolt-or they might break away from the city-either as immigrants or as 'refugees'! What happens would depend, on some part, to how you treat 'religious dissidents'.
8) As with espionage, later in the game, you should be able to conduct forms of 'religious espionage' within the game. Obviously many of the missions would be very similar to espionage, but with a religious bent to them! Not sure exactly how this should work, though!
9) Some possible religions would be 'Totemism', 'Ancestor worship', 'Paganism', 'Spiritualism', 'Polytheism', 'Eastern Religion I and II', 'Early Monotheism', 'Late Monotheism', 'Baptist', 'Blood Cult' and 'Ecumenicist'. Obviously you'd be able to add as many, or as few, religions as you wanted-through the editor.
Anyway, those are my thoughts on the subject, hope you haven't heard it all before

!
Yours,
Aussie_Lurker.