An Idea:
Instead of adding pagan religions as 'religions' we could add them as perhaps great wonders.
Now then, I am thinking the wonder code might allow this, but if it doesn't, I think I can make it;
Now then, have a couple of 'Polytheistic Church' wonders, perhaps 3 total that can be built. These wonders give the following benefits:
+1 culture/happiness per obelisk in a city with no religion,
OR
+1 culture/happiness per obelisk with no state religion.
and then the wonder itself provides +4 culture, and obsoletes with...something
That way, once the 'modern' religions get here the polytheistic religions automatically go away sort of, but the wonder keeps contributing, which in a way represents how the modern religions were influenced by the ancient polytheistic religions.
EDIT: accidentally pushed enter, I might not be done talking my head off yet.
Or if the 'until a religion comes to the city' modifier works, there is the possibility we could just have a 'pagan temple' building, (or there is also the possibility that a simple python event could 'remove' the temple from the city when a religion comes into the city or converts the temple into a temple of the modern religion.
Now, as for the modern religions, I think THIS would be a good list:
Christiantiy
Zoroastrianism
Islam
Hinduism
Judaism
Buddhism
Daoism
My reasons for removing Confucianism: I associate Confucianism less as a religion and more as a set of philosophical beliefs. Furthermore I don't see there being a formal 'Church of Confucianism' however, I admit I know next to nothing about Confucianism, so I am likely wrong about this. If so, someone who does know please tell me.
AND, even if it is a good candidate for a religion, The game mechanics would better work with just one religion in china, as currently there are 4 religions for 2, possibly three (Japan) civs, and that doesn't work so well.
OR, the Judaism as a wonder would actually be a very good way of representing it, as Judaism was never a large political force with the possible exception or recently, or as the standard scapegoat of Christianity, or certain fanatical rulers, to the best of my knowledge at least.