I'm very disappointed that religion is out of the game, even though I didn't necessarily like the way it was implemented - i.e., the fact they were all equal and that they gave science bonuses instead of penalties.
I think each religion should have had some kind of tolerance variable attached to it, which would determine the degree of its influence inside a civilization. That variable may vary, but only gradually (perhaps by means of the player allocating resources for "propaganda", which determines how fast that variable changes, and the player decides whether it is in the direction of more fundamentalism/more religious freedom).
For example, if people took the religion seriously, they would be very intolerant of other religions - as well as, to a lesser degree, moderately-practiced religions depending on the religious fundamentalism variable; hatred of atheism (with it full-science bonuses) should be set so that it is even greater than that of other religions, but the civilization hosting that religion with a high intolerance would gain bonus units such as suicide bombers (for Islam), inquisitors (Christianity), as well as other offensive bonuses, but at a huge expense when it comes to research and culture. At the opposite end, an atheist civilization, you would get apathy and war weariness, but a huge boost to research and culture.
Also, communism, nazism, nationalism (fascism) and environmentalism should be treated in-game as religions of the industrial or modern eras, each with distinct bonuses but with science and other penalties. For example, environmentalism should generate unhappiness and even riots every time a settler establishes a new city or cuts a forest, etc, nationalism/nazism should generate unhappiness from other nationalities inside civilization borders, and all religions should generate unhappiness of people of other religions (or atheists/secularists).
What I don't like is that Firaxis seems to be going the politically-correct way by not reflecting the negative aspects of religion in Civ, as well as not accurately modeling ideologies of all kinds - for most of its history, humanity was (and still is, although to a lesser degree than in the middle ages) driven by parasitic ideologies on the one hand and science and art on the other. No accurate simulation of history can be made without taking both aspects into consideration, although I am aware that doing so would definitely negatively impact sales. Perhaps there is still a possibility for a mod that does what I just said.
