How Religion SHOULD be done.

[Hypernova]

oh how clever

I mean, there's no WAY jesuit preists built Europe's greatest universities.

Universities were built by those who had money and power. They had long since stopped being run by the Jesuits by the time they had got round to teaching sensible subjects, rather than just theology and Ancient Greek medicine...

Taking a look at the realities of history, atleast in reguards to christianity it should be a bonus rather than a penalty for those things you listed.

All religion, and especially Christianity, greatly resisted change including all those things.

Providing an example of a religious society along with progress it made is actually very stupid, because if you look at the details often that progress was made in spite of rather than because of religion. Since religion was so prevalent in prescientific times, any advancement is bound to be have been made in a religious society, by religious people. There are mountains of examples of religion explicitly stopping progress, right up to the present day in fact. But it seems explicit examples of religion intentionally aiding progress (not just incidentally because it holds most power and wealth, like Jesuit priests founding early universities) must amount to only a handful at most.

religious people tend to be happier based on studies and research. Culture should also get a bonus.

Care to provide the research? Actually prosperous countries tend to be less religious, with the US something of an exception. Scandinavia tends to score very high in terms of happiness and HDI (Human Development Index), even compared to other developed countries, and it is the least religious place in the world. There is even a negative correlation between religion and education, especially scientific education (surprise surprise ), which isn't to say there are no smart devout individuals or dumb non-believers, it's just a correlation. Indeed, this may be why the American religious right produces scare videos about the evils of college.

I'd rather religion in Civ not be specific, in reality the religious beliefs of individuals were very particular to a time period, even if certain vague concepts remained unchanged, they were interpreted according to the social climate of the era. I certainly don't want to pursue religion for the great benefits it will lavish upon my empire.