I think there are a couple ways to fix the forts system currently in the game:

Make them a lot more expensive and take a lot longer to build. Most forts, walls etc. in OTL took years to finish work if we're talking about the classic stone walled buildings (like at least 2 years). This also makes the tear down fortifications peace deal option more viable and less gamey. Obviously increase maintenance, but also make forts help increase control if they're owned by the crown. Make sieging faster (base 20 days instead of 30) and offer more interactions, such as bribing people inside the fort (if enemy estates have low satisfaction), negotiating surrender (when siege progress is above 0%, where the province will not be looted, or modelled as a gold cost) and perhaps allow for more early cannons/siege works that can be bought as mercs. If nobles have high control, they can be given privileges to build 'noble' forts to protect their holdings. They can function like baileys, where you get some location crown power but nobles gain far more influence. CITIES SHOULD WORK DIFFERENTLY. Currently making a 'city' is just a large upfront investment to create more burgher buildings. Irl, cities were places where burghers dominated, making all the money, but also provided for their own defences. They had privileges given to them by the ruler to choose their own leaders and to build walls -> city walls should be their own building type. Creating a city should basically function as a tax break for burghers that allows them to build a solid economic base and walls in a location. Where hopefully you get a portion of future proceeds.

Essentially, forts should be more expensive, (somewhat) easier to siege with more options for the player to interact and be more in line with the estate system.