Egyptian=Kemetic, Greek=Hellenism, Norse=Asatru, Aztec=Teotl
I'd already looked into that, except I'd use
Olympian instead of Hellenism for the Greek pantheon; besides the fact that "Hellenic" just means "Greek" in their own language, I'd want to represent that the Olympian gods were not only the Greek and Roman gods, but they also were the foundation of many other mythologies (like the Celtic one), simply from the Roman influence in those areas. One possibility is to make these explicitly geographic, as in "Mesopotamian" or "Mesoamerican", but I'd rather focus on the pantheons as self-contained units that can be assigned to any civ.
Also, "Asatru" is a modern word for the 20th-century revival of that form of paganism, sort of like Druidic worship (which has very little in common with the original Druids), and is very focused on the religious side of things and less on the mythology. Since this mod focuses on the mythological side of things, I might go with "Valhallan" or something similar.
The core question is which of the following I should do:
1> Keep my mythology content as a completely unique system, unconnected to the religions. I'd have to do the renaming you described, but nothing else would really change. That is, you could play a Christian Olympian civ, with the various Christian bonuses from the expansion, and with the Greek mythological content (gods, foci, pantheon units, etc.). There'd be no explicit overlap at all between the two systems, except that I'd tone down my bonuses and penalties a bit to keep it from being too overwhelming when combined.
On the bright side, this would require the least work to make a version that players who don't buy G&K could use. But that may just not be possible, so I'm not really considering it a real advantage.
1a> Now, I might do #1 and still let the two share the underlying resource system. That is, the current Favor system would instead use the core game's Faith yield, allowing me to drop a ton of the bookkeeping logic. I'd expand the Faith system to generate through my four methods (Buildings, Specialists, Battles, and Base) instead of just the single system the Faith system looks to use, and adjust the costs of things accordingly. What this'd allow me to do is make Favor into a strategic resource to use for Mythological units and "spell" abilities, more like how it's used in the AoM strategy game. Instead of Myth units being explicitly limited to 1, 3, or 6 units per player, I'd simply make them cost one to five Favor resources, and have certain religious buildings create Favor.
The downside is that I'm not sure I could keep the existing Focus-specific Favor allocation if I change to Faith. Or I COULD keep it, controlled through Lua as it is now, but that'd remove a lot of the advantages of using Faith in the first place.
2> Add this content as another layer to the existing religion system. So when you're adding various levels of belief to your pantheon, there'd be one to three more layers to pick an entry for, which'd control the mythological content you use. Maybe one layer would let you pick which set of deities your religion can use, while another would control the mythological units/bonuses/Events and a third would control Favor generation. So maybe you pick Christianity, then choose to go a x3 Building, x1 Priest bias instead of the default Balanced (2/2/2) system, then pick the Kemetic set of gods/Events/bonuses/uniques. The result might not make much sense, thematically, but it should be balanced. It could even be a single choice at the start of the game; at the start you'd pick your pantheon, which'd persist until the Enlightenment and would modify your events, biases, and so on, all behind the scenes.
I don't know enough about the specifics of the two systems to know how easy this'll be to do. And if I went this path, I wouldn't want the new categories to be too much more complex than the existing ones, which might require some simplification. The biggest drawback here is that I'd probably have to drop the 21-Focus system entirely, rolling the effects into various choices within the religion system.
3> Add this content into the existing religion system as-is. That is, picking Hinduism as your religion would automatically give you access to their Pantheon units, events, and so on. Taoism would give the Shinto bonuses, that sort of thing. The first problem with this is that they're implementing several religions (like Christianity or Buddhism) that I just don't have mythological analogues for. But the biggest problem is that if it's anything like Civ4, then the game will allow you to change religions mid-game. My mythology design just is not built for that.
The common problem with all of these options is the Technologies. I rearranged the first four eras of the tech tree to make room for 15 new techs, and I'd prefer not to just toss them out. Besides just being nice to have, in general, the tech-based setup leads to a very specific effect at the Enlightenment, where you have to choose between delaying it to take advantage of the high-end Myth content and taking it ASAP to remove the penalties. So if I do try to merge the two systems, I'd still want to keep the Enlightenment in there somewhere as a way to disable certain parts of the religious content, sort of like how the "Free Religion" and "Empancipation" civics in Civ4 changed the entire game. I'm not sure whether that'll be possible, but it'll depend on how many techs (if any) the expansion adds and what it does to the early eras' timing.
Anyway, we'll see. When the expansion comes out, I'll spend a couple days just fixing things to stop breaking, and THEN I'll spend a couple weeks playing the expansion without mods (or with my Base+Empires for balance changes) to see what parts I think I can work with. So the first real post-expansion version won't be out until the end of the month.