Civilization V Announced, Now With Hexes!

[Weltall]

I would like to see religion done as an organic thing. Instead of "discovering" Hinduism with your scientists (a concept which is, frankly, absurd), make it so that you develop Religion over time, and its aspects reflect (and influence) your style of gameplay. For instance, if your civ is strongly-unified, your religion will tend to the monotheistic, whereas a geographically far-flung and disconnected empire will tend towards a more populated pantheon. If your early game involves a lot of combat, your religion will develop aggressive dogma whereas a peaceful early game will develop more of a philosophical dogma. This can therefore influence scientific development (in which a nation worshiping warrior gods will gain militaristic advances quicker but take longer when researching economic advances).

Another thing to factor would be that two nations which share large borders for long periods of time will have religious effects bleed over into one another even if their religions develop along fundamentally different levels for a long time, or create a situation like Christianity (and later, Islam) which take a similar religion and drive it in a radical new direction.

You can therefore lead into a situation as in Civilization IV where nations with similar religions enjoy stronger diplomatic ties, and a situation in which one nation will be considered the center of a particular strain of religion and enjoy an advantage, or end up creating schism and lead to religious strife.

And, atop all of this, make it so that the religions can become very similar to those we know, without expressly identifying them by real names.