fearuin
Born to be Warlord
Consider having 3 'shrines' for each religion (for example, christianity could have the temple of the nativity for orthodox, the vatican for catholocism, and perhaps the cathedral of cantebury for protestanism). Each shrine allows that civilization to build orthodox/catholic/protestant cathedrals in cites that have a christian temple. These cathedrals can produce a maximum of 3 happiness: 1 for having christianity as the state religion, 1 for having thier shrine within you empire, and a final happiness for a 'favourite' civic of thiers (eg Org religion for orthodoxy, theocracy for catholicism, pacifism for protestanism). In this way, different religious authorities 'pressure' thier respective civilizations to to adopt different civics, leading to differences between empires within a single religions, and, in due time, religious wars. This concept does rely on the fact differences in civics wil cause antagonism between civilizations, but that isn't hard to mod in and would probably more accurately reflect the 'differences' that real civilizations have found between each other.
If you can mod this, I'll start worshipping you! (And today I've woke up as an atheist ). But we will have to find 3 sects to every religion. It won't be that difficult, but I'm not sure if every religion does have them (e.g. confucionist sects? I only know legalists as their major doctrine...).
About zoroastrism, I'm still very dubious about it. I know they had a lot of influence, but... this faith has almost died. However, I have a simple idea to make zoroastrism, or, as I proposed earlier, a generic solar polytheism, (I still support this idea) become "fading". It simple: make their missionaries, temples and monasteries obsolete with a certain tech (e.g. Theology, or Divine Right). We can make the religion itself to have a low spreading rate, also. That way, ONLY if you built the holy shrine, it will have a chance to continue expanding, and anyway, it won't do it very much.