I wrote a post earlier, but I can't find it now.
I had the same idea about Ports - should be possible to fortify them with arty AND infantry. Likewise, ships should be able to levy crews against them. It would be amazing if there was a 'food' value for a ship too. Big ships could have a lot of food for many turns. Eventually, all ships would have to return to ports quite regularly. Of course this is made a bit awkward in Vanilla which has 2 turns per year, so it's not uncommon to have ships sitting in one location for 80+ years. I guess the idea though (especially with trade ships) is that this is where they are stationed and the ships are merely representations. It's not that unreasonable for a ship to start in one location and sail back and forth to their home port in 6 months (In spite of the fact that it might have taken them 2 years to cross from the Atlantic to the East indies...). It's just tough to rationalize single level combatable ships with their campaign map counterparts.
Anyhow, I would also like to see weather take more of a role too. Large meteorological systems such as localized heat waves, variable snow covering that impedes map movement. Certain units that are better at moving around in certain weather conditions. It's already half there with some units being better with certain types of battlefield conditions and a few units that can move better in the wilderness areas. But not enough.
One of the biggest things I'd like to see is 0 turn militia/rabble/mob units and VARIABLE SIZE units for 'undisciplined' troops - based on population. Further, it would be amazing if we could recruit certain types of troops in some of the other buildings. It's not unheard of for citizenry to take up arms - these types of troops are already in the game. But it doesn't really make a lot of sense that they show up in 200 units or whatever.
I'd love to see churches able to recruit working class rabble, with the size of the force being based on the size of the church, the population level, and the richness of the town would determine what their armament type would be. IE:
Large church in a rich town in a high population province - Recruits mob with approx 150 units, using mostly hunting rifles, almost as good as line infantry stats, with high morale, but no special combat abilities like fire by rank.
Large church in a very poor town with high population - recruits mob with approx 150 units, but using mostly farming implements. Strong morale, good melee unit with low attack, but good charge bonus, but well suited to the terrain.
Small church in a growing town with low population - Recruits mob with approx 40 units, using mostly longbows, Medium morale, low melee attack and poor charge bonus.
Each step of church would allow one more unit of recruitment. Units could be 'called to action' rather than recruited. Pay a small amount of money and they form up instantly. Use very low upkeep, but have their morale drop 25% each turn that there is no enemy in the home territory and when it hits 0, they disband and return to their homes. Also, while units exist, the effects of the building that trained them are halved. These mob cannot leave home territory and they are tied to the building, so a building can only train so many.
Of course, you could have similar units for other buildings. I would imagine that people that frequent taverns would have a slightly different characteristic than church going sheep, so you might find a little bit more powerful units - although probably lower morale. Less farming implements, more cudgels, knives and pistols.
Likewise, farms and occupational buildings would field strong, but not well armed, nor high morale troops unlikely to have advanced weaponry. Access to chemicals would probably indicate that the better of these could field some makeshift grenades, but with less range than grenadiers (I'm a fan of increased range of all troops, although possibly not as dramatically as DMUC). Might be fun to see a unit with chains for the poorer towns. Farms would likely have access to horses as well - and possibly wagons. Could be interesting if these guys could build fences.
Schools would yield smaller units in general, but significantly more skilled and possibly armored. Would be really fun to see a good variety of units in schools, maybe including mini trebuchets, crossbows, double barreled rifles/muskets, possibly some of the smaller scale, simpler artillery units as well, maybe a mini-mortar or an early model of rocket with direct fire, fire arrows, quickly deployable traps (Caltrops, small mines, smoke bombs)... Also, gentlemen cavalry, armed with pistols and a sword.
It could also be possible to add factors such as happiness of the city (note that this can already be affected by the presence of enemy troops).
This would add quite a strong level of sophistication to raiding. It doesn't really make any sense to me that a shattered 4 soldier unit can go around raiding the heck out of Palatial estates and such with absolutely no resistance. It also doesn't make much sense to me that the 'mob' citizenry doesn't seem to really get any stronger, regardless of how well or how badly you are doing.