I would love if the pop points had the "culture" of a given civ (or a minor faction) assigned to them, even though it would involve some clever dealing with the balancing of such things as the speed and degree of assimilation. After all IRL you have crazy and hart to intuitively comprehend differences in the resilience (or lack of it) of the particular cultures, with some seemingly "powerful" ones disappearing after few scant centuries (see Mesopotamia, ancient Egypt, Greks in Anatolia, Nubians, Chams, Roman Punic culture etc) whereas other survived for millenia. Also I would hate to see the system making it trivially easy to just "convert" other cultures, I'd much prefer the process being very slow and unreliable and you rather having to deal with the cultural diversity. Also such system would naturally facilitate separatist rebellions and emigration. Like how the hell can the 4X game series have straight no rebellions?
As for the loyalty system, I hated it because it was simultaenously annoying to deal with, difficult for the AI to handle, and being based on absolutely nothing in history. I mean states have always been based on the military control, and switching of territory between them on diplomacy - show me when could a province of some strong, functional empire just spontaneously leave against the will of the emperor with no military action being possible to prevent it. Just make it like in Paradox games, where a province (city) can revolt to change its owner but its owner has a window of time for the military supression, so said province either has to win militarily or revolt in the time of weak central authority.
Also I'd like to point out that if the loyalty system were nuanced and interesting it has to be based on city happiness not population, but if it is based on city happiness instead of population then it can't fulfill its function of dealing with the AI forward city settling. A function that has always seemed strange to me because it was the problem of the way territorial control and colonization works in those games being solved by an entirely different system. Instead of, you know, simply programming AI not to do this clearly suicidal idiotic thing, or changing the way colonization and territorial control work, so for example inland cities with no sea access have to be founded in the continuous way within a certain distance (it would make a great deal of sense and look better anyway).