Yes indeed

Your ideas are so good, will balance for sure a forgotten task like the religions.
Building a empire is not a easy task, people have to worry about great expansion, many things can destroy the empire from its hearth.
Religions, schisms, unhappiness, to balance people unrest in not balanced empire will be needed martial law, means a lot of armies stationed in main cities.
I am thinking about federal states to stop problems of colonies unrest, with lower taxes.But Schisms are important a lot, fragmentation of a state religion is a important factor, hard to control.
Is very important to have a control panel of religions, with percentages for cities, growing times in %.
But this a so big mod that i am a little worried to talk about

so many change; people are more concentrate on growing armies, more then look for culture or happiness of his people, so rewards to look at religion are a must, special units buildings and wonders are needed.
"When a holly city is captured by a civilization with a rival state religion (Like Muslims taking Israel), Relation with nation with the holy city religion will worsen (igniting crusades )"
Thats a great idea, and perhaps will generate a possible alliance between nations of same religion.
i am thinking a lot about crusades and their impact on civilization, Knight Templars, Knight Hospitallers, Teutonic knights and the Order of Saint Lazarus, they glued the western Europe with a common goal.
They can build road, castles and fortress, and hospital to heal faster army far from cities in enemy countries or less controlled areas , i think to special unity with workers task and special promotions.
Relic is an object, especially a piece of the body or a personal item of someone of religious significance, carefully preserved with an air of veneration as a tangible memorial. Relics are an important aspect of Buddhism, some denominations of Christianity, Hinduism, shamanism, and many other personal belief systems.
So archeology becomes a tech to study to find relics so the religion have a one more way to spread, i feel always weak when i need to diffuse religion, we need free converting units for reward with the grow of religion.
You have so many cool ideas about religion and i can help so little, i am not xml programmer, i can only make 3d models to eventually help you but is a little contribution.
i like when a civilization grows and the problems related to have a big empire impact economy and treasury, big armies need a stable empire, the fall of roman empire was mostly internal, and the grow of roman empire was a need for the population of medieval ages.
Anyway thank for your so exhaustive answer, let's continue to dream about a religion mod inside Overlord, when you dream a lot about something, is possible that a dream becomes real
