I think this was basically how Advanced Temples worked a long time ago. Each civ had 2 versions with unique abilities, and you could not build both in the same city.These were removed in version .16, so I've never actually played with them. They sound like a great idea to me, and I'm not sure why they were removed.
I'm planning to reimplement advanced temples in my modmod, similar but not identical to how they were originally. For example, one Order advanced temple will grant the Inquisitor promotion (which will have higher prereqs in my modmod) to all disciple units built there.
copied from my (outdated) Future Additions/Considerations for Later Versions post in my my modmod thread:
I'm open to suggestions about how best to implement these.