Given how Civ VI will apparently be 'un-stacking' cities just as CiV did with units, I think it'd probably be best to start work with one of the smaller-scale mods (probably Rhye's of Europe) before attempting the full scope of world history with a full scale world map.
I'm not sure if this idea belongs here, but I was putting more thought into a Europe-history mod, specifically into how to allow (much) larger maps without overwhelming the game with lag. Given the needed map size to make city+districts work within a standard European map context, I think the best thing would be to allow more cities with fewer units overall. This could be as simple as making units much more expensive and buildings much less so -- which fits the historical reality, since it'd be pretty easy to find a farm or forge in medieval Europe but castles were pretty rare and armies were smaller than in later ages.
However, I had another idea, that I like quite a bit more. One of the things that the Civ VI developers have been talking about is that this new game 'unstacks' cities (with districts) just as Civ V 'unstacked' units (with 1upt). My suggestion would be to correlate specific units (usually the more advanced ones of each age) with specific districts as prerequisites.
For instance, a recent gameplay video shows a city making a new 'trader' unit that generates a trade routes and builds a road connecting two cities. I'd propose that building such units should require the city to have a commerce district (and possibly a first building within that district, like a market).
More obviously, you could require a barracks for more advanced infantry, an arsenal for more advanced gunpowder/artillery units, etc.
For a mod centered around European history, you could do something even cooler.
Say you could upgrade normal improvements, just like you can apparently upgrade/expand city districts. Farms, then, could be improved initially with manor-houses, which would give bonus commerce. Later on they could be improved with castles -- which might give defense + immunity to razing, but would also enable knights.
For each farm+castle, that city could produce a single knight.
If you wanted to limit it further, you could connect farms to how many hitpoints each knight has:
- The first castle gives a single knight with half its normal health as its maximum
- The second castle boosts that knight's max health to full
- The third castle allows a second knight at half-health
- The fourth castle boosts the max health of the second knight
- The fifth & sixth castles would perhaps provide a "Squires" promotion, that allows the unit to heal more quickly after combat
In other words, knights would retain a consistent pre-determined strength, but the size of the army (reflected in its health or hitpoints) would depend on how many castles exist within that city's region.
Another restriction could be based on the historical tendency for armies to 'live off the land' -- a nice euphemism for looting and pillaging from whoever was unlucky enough to live in that area. This could be included by reducing the food production of each tile with a unit on it to 0.
Whichever path you take, I think that restricting units would do quite a bit to limit the turn-by-turn busy-work that makes the later game go so slowly.