On the one hand, I think that rebellions as described by Ailfertes would be a good idea from a historical perspective, as well as for the AI. However, a big problem would be the (relatively) low speed of armies. For instance, in EBI, it might take a year for an army from southern Spain to reach Italy, or for an army in western Asia Minor to reach Syria, much less Egypt or western Iran. Not to mention, starving a city out (to avoid the horrible siege battles) takes two years by itself. Ideally, one would be able to march through friendly territory much more quickly than one does enemy territory, but the game isn't built to do that.

Regarding Moonburn's loyalty system, wouldn't that just result in the player having to spend a lot of time and effort mechanically rotating family members from one city to another? Is there any actual challenge to doing so? It would be fairly easy for a player to come up with an "ideal" rotation of governors, but they would have to move each individual family member back and forth, probably over multiple turns, for in-game decades or centuries! It's mind-numbing enough distributing governors among a 50-province Roman Republic, without having to send them all back to Rome every so often (a trip that in-game could take eight to twelve turns of marching! And because of the "Forced Marching" trait, you have to move them just slightly less than the maximum each turn, or they start getting bad traits.) Also, I'm pretty sure that the council idea is impossible, because you can't add another button to the UI, or have independent Ancillaries.