Civic specific events as well as religion specific ones are a must (at least eventually). We can already take the slave revolt event for the slavery civic, plus come up with many more(better ones) of our own. (I would personally prefer if your succession event had another option-turn the city into a colony) The Holy mountain quest fits well with RoK, and the Sacred sea equivalent with OO (Still, I suspect that they both suck compared to the quests specifically designed for FfH)
Personally, I would like the "AV and Order religions can't co-exist in the same city" mechanic to be replaced with a more general "religious riot" type of mechanic (perhaps implemented as an event, perhaps not). Each religion should have a different compatibility with each other one (e.g., The chance of a riot between the Order and the Empyrean is very small if not 0, but the chance of having problem between the Order and AV or between the Empyrean and the Council of Esus is nearly 100%. Other combinations would fall somewhere in between.) Whenever such a riot occurs, the city goes into unrest (as if it had just been captured or as if Purge of the unfaithful was built there), and stays in unrest until one of the conflicting religions is removed. When in unrest, there should be a small chance each turn that one side will be victorious, eliminating the opposing religion from the city (and possibly reducing the population in the process). This could drag on for quite a while, but an inquisition could bring it to a sudden stop.
I love the idea of promotions that strengthen a unit, but limit it to traveling on certain terrains. Great idea, I wouldn't mind seeing it extended to other powerful promotions/units with their own unique movement restrictions.
The mention of limiting units to moving in hell and discussion of hell resources reminded me; we really need to get a hell version of water tiles pretty soon. I know you were disappointed that you couldn't make hells' rivers run red with blood, but that is no reason to not make hell terrain,if only to let us know where hell is spreading. Besides, the civilpedia already describes hells seas not as red, but as black, completely smooth, and reflecting stars not of creation. I'd love to see black water with randomly twinkling colored stars shimmering on its surface. The flavorful effects of upgrading specters to wraiths and occasionally causing units to turn barbarian would also be nice. Even though not mentioned in the civilopedia, I for some reason picture the coasts of hells oceans instead only a little darker, tinged with a sickly green hue, and covered with a thick layer of fog which may extend inland a little. Undead ships like the Sailors dirge would be quite fitting here (perhaps ships at sea that turn barbarian should become undead, start generating skeletons, and patrol the coasts). Lets not forget unique Hell resources. I'm thinking sea serpents and cephalopoids are in order.
I don't expect any of these things to be implemented immediately, but they could be nice once we actually get into Shadow.