You can't compare trading nations and kingdoms. Genoa's and Venice's reason to have land a few settlement a little bit far away was because of the trade. I don't think it was so god damn hard to hold a settlements, and why should the population even care if they were treated well? I would certainly not rebel if i were treated good and i think Genoa treated their far away land good or then they couldn't hold Caffa and Azow. Venice however had a stronger navy and military force, so they could of course hold their Greek provinces more in the way they wanted, still they fall to the Ottoman Empire because of the Venetians intolerance. Even the god damn Orthodox patriarch supported the Muslims instead of his closer related Catholics.
If one is used to and has invested in a certain way of life which accords certain privalages requiring a near and accessable governmet. Some distant fool who says this is mine would be bound to aggrivate people into action. Despite Nationalism being considered the core of fascism many people throughout history do not want to be united with their enemies except as the rulers of said enemies. Hence many revolts. Think about what Machiavelli says. Men must be treated well or destroyed. Currently in game you stand arround and do "beeb" all for 50 years suddenly it is yours without difficulties. Then you can easilly change religion and can count suddenly on all taxes being promt and paid. That is not the way it should work in the game because in real life it sure didn't.
I dont see the problem in asking for realistic problems to be faced by the ai as well as the human requiring action to be implemented as the worst choice should be do nothing.
If we talk about Venice and Genoa, look at how many problems they had in holding their regions. The locals did not want them unless they were colonists, as such either a revolt would find ground or in the case of effective (effective not good) administration half hearted defense against another more local power was given. Is it realistic for Castile to support colonies on the Black sea cost next to Wallachia and not be attacked whilst it also tries to conquer North Africa.
I think that the further away from the capital or general provinces the harder it should be to administrate provinces and the harder it should be to supply a Navy or Army. It is not like any Empire was easy to form.