It's not really a big deal, and I'm not sure if someone's mentioned it, but I noticed a few counties that have anachronistic names. Pelegiad in Vvardenfell for instance. From what I understand, the county was named after an emperor that didn't exist yet. Also, Frostmoth wasn't built until the third era. I suppose, though, that if you conquer it as the empire, you're essentially accelerating the time frame, facilitating it's earlier establishment. My knowledge of the provinces that weren't in ES 3-5 is limited; So I haven't noticed any others. Maybe the names could be blamed on a dragon break. =P
Also, I've never been the dragonborn other than cheating to see the mechanics, but is it possible to add an event where the Greybeards summon you to High Hrothgar when you become the dragonborn. Or add a similar decision when you reach a certain age and are dragonborn. Maybe even add a very rare event after the establishment of the Empire and vassalization of Morrowind and Vvardenfell that create a once a game Nerevarine. It would also be nice to have a decision to separate the kingdom of Orsinium from High Rock if a player feels so inclined. Lastly, is it possible to reset the year to the 3E:0 upon creation of the empire and assimilation of all Tamrielic provinces. If these are already in the mod, or they sound too ridiculous or difficult, just ignore them.