So far my biggest issues have been:
1.A lot of abilities don't work: A lot of the descriptions are just plain inaccurate, like the Dwarves getting a trade route from industrial zones, and in general the bugs are all over the place. Many people in the comments have mentioned them if you plan on doing any fixes.
2.The default civs are still in the game: You can choose to pick the civs in the game and keep them out that way, but I would rather have some randomness involved instead of having so much control over my scenarios.
3. Civs are boring and repetitive: Honestly when picking any of these civs, especially the ones I don't know the lore for, I find myself uninvested in their abilities. Many are copied straight from civs in the base game or are weird patchworks of them. Fine, as long as it's appropriate, but here most of them have the same few abilities like +5 strength on the continent or bonuses to tundra. Each civ's bonuses should encourage a unique play style. Even if the abilities aren't necessarily good outright, as long as they promote some engagement from the player and have the potential to be great, that would be enough.
4.Some civs are overpowered as hell, or underpowered as hell: Many of these civs are so overclocked it is insane, like the Dunmer or Altmer, who have several beefy unique units and unique improvements that let you just plunk down an incredible and worthwhile defense for cheap. On the other hand, some like Organum have next to nothing going for them. The only thing that gives anyone even a semblance of balance is that certain abilities just don't work. Also, less fort improvements please; everyone's defense is waaaay too strong and uncompromising to make conquest interesting or dynamic.
5.More unique buildings and districts: Along with the unique improvement problem is the fact that civs either have a ton of unique units or improvements. Less than a handful have unique buildings or districts. Combat is fun, but units get fazed out and at that point you might as well play a vanilla civ for the rest of the game. Improvements that double as forts aren't exactly that great either as, not only are they repetitive, but more often than not forts are supposed to be a tradeoff for resources. China only gets the fort bonuses because placing a worthwhile set of wall tiles leaves little room for other improvements, so it evens out. Here you can dump them anywhere and plonk down a fully fortified unit to give the finger to any invader. Buildings and districts make these things more fun, by interacting with them and forcing you to be creative with how you build your civ and how you go about conquest (see Phoenicia or Poland for good examples of this).
6.Technology and Civics should be reorganized: The thing is, TES is a medieval fantasy series meaning that when you hit the Renaissance and Industrial eras the leader screens remain the only thing recognizably TES. I'd say if you want to keep tech and diplomatic victories(and you should) maybe change the layout of the tree, maybe taking the stuff from earlier civics and spreading them out to fill up a few more eras (this would mean replacing, removing, or downright altering Renaissance onward techs, but means you wouldn't have to create a bunch of new stuff either). This way the integrity of the game can remain, but the pacing would improve and the massive amount of unique units would not get phased out too much. A great example of this is in the Civ of Ice and Fire mod, where there is a medieval era end date, and all of the units have upgraded versions of themselves to keep each unique unit viable.
7.Immersion: This is something that can be remedied by following some of these last points, but also by adding in some more flavor text. Change names of districts and buildings, basic units names could alter or their icons can be replaced, and each civ leader might have a unique way of talking (agendas also would be cool, though I can see they are being worked on). Even just putting in low poly models ripped from Morrowind or whatever for the unique units would be welcome. Just a few little things could really make this point a non issue.

That's it, that's all I have to say. Again, A Civ of Ice and Fire mod would be a great point of reference should you choose to work on this mod anymore. A lot of criticism on my end, but I still play the mod and enjoy it, and I only type this because I believe this mod has the potential to be phenomenal. Thanks for reading!