Occupation

One thing that's bugged me for multiple civ games is how easy opponents will roll over for you. Especially in 6, cities are almost fully usable once you capture them, and become essentially fully yours when you sign a peace deal. Always feels to me that it should be much longer before you get a workable city out. My proposal:

-When you capture a city, it's in resistance for 1 turn per pop (as in previous games). While in resistance, you get 0 yields in the city.
-As well, any city in resistance, there should be a chance that the city or district rebels. For each district in the city, it should be about 50/50 in each turn if you don't have a unit on or next to the tile that it would rebel. If a district rebels, then whoever you capture the city from gets a new melee unit on the district tile, and the district gets auto-pillaged. If that happens to the city centre, then the city actually flips back to them. So if you capture a city at size 10 with 4 districts, you need to basically garrison 4 troops in the city for the next 10 turns to prevent any rebels from forming. If the city fully rebels, that can bring a civ back from the dead too, so you're not off the hook by wiping them out.
-Once the resistance period is over, then the city gets an "occupation counter". Say that counter starts at 100. What will then happen is:
--If the occupation counter is > 0, then the city gets 50% food and 50% production (similar to the current occupied status)
--The other yields (gold, science, etc...) are reduced by the occupation counter. So if the counter is at 75, then you get a -75% "bonus" to those yields.
--The counter will naturally decrease per turn. Also, it can decrease faster by stationing military units, or by having a large cultural or religious influence on the city. If the previous civ is wiped out, or they cede the city in a peace deal, the occupation counter will drop by a lot, but it will not drop to 0
--As long as the occupation counter is > 0, there should be a chance that a district could "rebel", however in this case, it would simply just get pillaged, and not spawn the units.

This way, if you want to conquer someone, you basically need to not only have the units to keep advancing the front, but you will need to keep units back to police the cities that you have captured. In a lot of cases, those may simply be troops that are healing up anyways, but it would certainly add another challenge instead of capturing a bunch of cities and suddenly seeing your tech rate double by capturing them all.

 

The idea of nation and people's war is rather new. (late 18th/19th/20th century)

In historical times most people were peasants without rights and were part of the land which often changed its owner as a result of war. Why should peasants worry if they are ruled by King A or King B when taxes are high under both kings.
Kings were often foreigners (conquerors or their successors or marriage partner of successor of old king, etc). By the time the ruling families formed Royal Dynasties, which can be regarded as an elitarian group of people who managed the principallities and kingdoms of the (european) world for centuries. By the time most dynasties were connected via (crossing) marriages, so e.g. in early 20th century the German Kaiser Wilhelm II and the Russian Zar were cousins. The German Kaiser was also a grandchild of the British Queen Victoria. Great Britain was ruled for a long time by the german houses of Hanover and Saxe-Coburg-Gotha ... Catherine the Great (Russian Empress) was a german princess, two of her cousins became Kings of Sweden. The house Habsburg (Austria) not only controlled the throne of Holy Roman Empire in Europe for some time but also Spain and its Colonial Empire and the Netherlands, ...
So probably most people most of the time in history were ruled by foreigners ...

An exception were small communities (free cities) which organized themselves in a democracy or republik, where free members had low taxes, a right to vote and trade and engage in politics. Loosing these rights/freedom often led to uprising/revolt.
Another exception is the force of a state religion or state culture (language) upon the conquered people which often caused resistance.
A brutal conquest may also increase resistance ... however in Civ games cities usually do not surrender peacefully on their own when faced by a huge siege army, so you would need to get the city peacefully in a deal from its former owner to prevent brutality and atrocities.

So if you capture/receive a city, it will take some time to organize it and get yields. Resistance should mostly depend on conquest, government system, tolerance, religion and taxes until one of the civs researches nationalism.

 

The medieval resistance in Italy against the Holy Roman Empire was massive. Machiavelli recognized and wrote this already in 1513.

I could imagine that the resistance might have something to do with the cultural strength of the vanquished.

 

I think it depends on personal freedom in a society. People fight to defend their freedom, not slavery and serfdom. You can go back in history to the mythical fights of ancient greeks against the persian empire.

In case of the Italian cities, I think they were able to resist since they were wealthy from trade, which allowed culture/art as well as city walls and an army, and they organized themselves in a league, so that they could field a combined, competitive army.
The willingness to accept a higher institution like the emperor ceases when you are rich enough to have an army and when the emperor most of the time is far away behind the alpian mountains. As far as I know they battled about who appoints the city gouverneurs, the cities (self-government) or the emperor ... since they challenged the emperors authority, he had to react ...
https://en.wikipedia.org/wiki/Lombard_League