Sorry if disrupting, but couldn't it been funnier by completely separating province/city? You would then have two kind of provinces:
-countryside, were your armies could be at the north or the south, meaning they have a range of control (economic and military) on the province (and a bit of a nearby province, in time of war). It will produce ressources such as grain, wood, wool, salt. They might also have spots for mines. You will developp them with roads, bridges, and farm/mine modernization
-cities, with a short range of action on a nearby countryside(it's not just a dot, you can't infinitely multiply their numbers.) They would be crowded like colonies(or to be precise, colonies would be small cities), by granting them tax priviledges over countryside, or by forcing people to go there.Their income would be from industrial production(or pre-industrial, if you prefer), trade of the goods of the surrounding countryside, and world trade maybe.
You could modify the income with the previous modifications of EU2 (tax collectors and manufactories, but specialise them more)and with the countryside roads.
Enclaved cities were not so rare, after all. Then you could, diplomatically:
-give a province without cities to a vassal, and it'll be harder for him to make a decent war against you if he tries.
-make war for cities, good sources of wealth, or strategic positions.
-grant a city to an ally(or an ennemy in a peace deal), most often a coastal one, which would be necessary for him to trade directly with you (you can still trade with a direct neighbor, but direct trade generates more profit to both ends, with less additions of tarrifs)), and where he could harbor some troops in time of peace(Think of trade privileges in India, China or North America, at the beginning). I know this might change trade structure. Or it might just be for a big outpost.
-force an ennemy in a peace deal to destroy a city fortress, or forbid him to build new cities or fortresses
-the owner of the countryside could have a CB for the city(ies) inside
But, we can maybe avoid countries without at least one city (the royal court), except for court feudal vassals (court puppets). They just get their income, and often plot together against the authority. They have less options than real countries. They heavily depend on the character of the ruler, because there is less "public opinion".
Free cities, with only one cities, are even more limited, and must be vassals of other counties, but could more easily be centers of trade and finance(foreign loans)
and you can have city states, with only an harbor as a capital, dominating other cities.
you could then have domestic options modifying the balance between city population and countryside one. Or some kind of interaction between the two (aristocracy-plutocracy, serfs-free subjects
Armies could then be located in a city or in the countryside like its done for harbors (with a limit, of course, cause a 20,000 inhabitant city cannot supply a 100,000 men army)
a network of cities with their range of controll could be done as a kind of big barriers. Army could still pass it, but at a very high cost, as they would either lack supply because the fortresses controll the countryside and their supply lines is an easy prey for raids from the fortresses, unless you leave most of your army covering the area.
and you could have rebels and brigands hiding in the countryside, like pirats (could be funded by other players?), harmering your trade, income and security, so that you'll need to keep patrols.
Please tell me what you think of it.
I might add ideas as they come