In my opinion, there is a way to incorporate Religion more, in the game, without offending anyone-and it doesn't even need that much new code to achieve (some of it can be done by editing the standard game!)
Basically, ALL religious "Techs" should be available in the ancient age, and all of them should be non-prerequisite. My ideas were for Early monotheism, which represents Judaism, Christianity and Islam; Eastern Philosophy-which represents religions/philosophies such as Buddhism, Taoism and Confucianism and Eastern Religion-which represents Hinduism and Shinto. The first religion would have a prerequisite of Code of Laws/writing and Polytheism. The second would be based on Philosophy and mysticism, and the third would be based on Philosophy and Polytheism! Please note that these are merely possibilities, and I haven't quite settled on what techs should be which. This would then allow a polytheistic faith, like Shinto and Hinduism, to survive side-by-side, into the modern age, with monotheistic faiths!! Give each type of religion it's own set of buildings and units, and suddenly religions do take on a whole new shape in the game

. The new stuff, though, would be to have a form of 'religious espionage'. This could incorporate things like the Sacrifice=culture idea that has been mentioned for C3C, but could also include a form of "Religious Propoganda" to help simulate conversion via cultural conversion. You could even set up a "Religious Embassy" or sabotage religious improvements of other Civs! All of these are reflected in Espionage, but there should be a seperate one especially for religion!
Anyway, that's just my thoughts, plz feel free to let me know what you think

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Yours,
Aussie_Lurker.