If you can create some sort of working uniform system for the way cities and forts are represented then we all owe you a big thank you.
On a similar note, I think that perhaps forts ought to require some sort of small upkeep - sort of like army and navy maintenance. Would it be possible to mod this in?
At the moment, it's just a case of improving all your forts as and when you have the cash to do so; short of choosing your initial forts quite wisely due to financial constraints there's no real reason not to fortify everything to max. If you have the money, however, you'd just upgrade them all.
Another thing is that - in keeping with the random event to de-fortify provinces - I think fortification should be tied to both province revolt risk and centralisation/aristocracy; by this I mean that the more aristocratic your realm is, the more you should be able to upgrade provincial fortifications (castles, walls, and later military forts) but as you become more plutocratic (particularly with republics) there ought to be negatives associated with large fortifications. Kings had their lords build castles to defend and oversea the surrounding area but as feudalism eroded these castles were destroyed (and in Europe a lot were destroyed during wars and revolutions) as the state held the balance of power over those who claimed to rule in its name.
My idea would be to - if at all possible - add a forts maintenance slider and tie it to the number and levels of forts you have. There should be an incentive to upgrade forts in particular provinces of strategic interest as opposed to simply upgrading every city. That way, we could differentiate somewhat between large, populous cities (which became de-fortified over time, as opposed to the opposite) and actual fortress provinces. I'm not saying the distinction needs to be immense, and clearly there were examples of cities or particular provinces with a large defensive infrastructure (such as Isle Royale and Gibraltar) but I still think it's a good idea if the coding isn't too complex.
There should also be some sort of incentive to de-fortifying towards the end of the game, and indeed to not spamming forts everywhere unless you can afford the maintenance costs - which would be noticeably for L5/6 forts - the end game, higher tech levels.
Just an idea. Please don't shoot me.

o
Austen
EDIT: As for the graphics above, I think a little number in a coloured box in the top-right corner of the image would work better than a coloured line. I think someone else posted such an idea in another thread, but I don't have it handy.
Oh, here it is:
I think something like that would look great. All those are good ideas.
Off-topic: As is this...