Have you thought about pantheons, beliefs, spies, ideologies and great works?
Religion will work like in normal game, but there will be no distinction between various types of beliefs (pantheon, founder, follower etc.) - you can pick any belief as pantheon, any 2 beliefs when you found a religion, and 2 more when you enhance it. Every belief will refer to a particular god, and will allow building temples to that god. Also I consider making some civs start with a pre-defined pantheon.
Ideologies will be changed to Alignments (Good, Neutral, Evil), but they probably won't be present in the first released version of the mod.
No espionage or great works (or tourism) for now.
Edit: Anyway I came up with some ideas.
Griffites- UU: "Conquistador", the same unit Spain have(might need a different name though) but can found city on same continent. I think this fits well with the Griffite theme of a civ of horsemen.
Actually it's the Dreamers civ that gets the Conquistador, as this is the expansionist civ inspired by the colonial empires. (They also get Conquistador Musketman, an advanced recon unit.) The Griffites are more like medieval kingdoms - they get Knights as one of their UUs.
But the Conquistadors don't get the ability to found cities, as this aspect of the game is changed - unhappiness from number of cities is greatly increased, unhappiness from population decreased, and you can't build Settlers, but you get them for free when you have enough happiness (this helps the AI a lot in maintaining the right pace of expansion). What I want to achieve with this system is better balance between players (no "runaway civs"), and maintaining some wilderness where barbarians and monsters can spawn, through the course of the game.
Archon- UU: "Holy Legion" (you probably had something similar in mind), basically the same as the roman vanilla version(when I say vanilla I mean, un-modded BNW), but some faith gained when it kills another unit.
They have both Legion (which is similar to the vanilla game version), as well as Crusader, which can be purchased for Mana*, and gets Mana for killing units.
* renamed Faith, as it will be also used for magical purposes, not only religious
Vodniks- UU: "Shore Dweller", unique worker that can build boats, like Samurai in vanilla. Plus it can "build" marshes, but only on grassland with freshwater source next to and there must not be another marsh next to it already.
Interesting idea - perhaps in can be a unit that performs the functions of both Workers and Work Boats (but without getting "consumed" when building a Fishing Boats). About planting new features (marsh for Vodniks, forest for Elves, jungle for Lemuria) - I'm definitely going to add such possibility at some point, although there can be some technical difficulties.
Snobar- UB: "Meadhall", I don't have any good bonus ideas, maybe some bonus XP for melee units, since they got inspired by the stories of great valor in battle, they heard at the Meadhall.
Good idea, noted
Azracs- UI: "Pyramid", give some bonus culture or faith. Must be built on flat desert, can't be next to another pyramid, take a lot longer to be built then other basic improvements. Maybe the graphic feature that shows up next to the city who builds the vanilla "Great pyramids", can be use as graphic for such an improvement.
Actually I gave them another desert-only improvement, something like the one Morocco has. Various "Ancient Structures" (including Ancient Pyramids) will be generated on the map at the start of the game (I don't know how to use wonder graphics, so I will use El Dorado graphics for now).
I have a similar idea for one of the civs (not in the current list of 12) as you for the Pyramids - it will be a civ that can construct special statues, that will produce culture and mana, and give a combat bonus to nearby units.