I'd like to see earlier "Corporations:" Hudson Bay Co. The Dutch/British East India Co. are historcial examples. The British East India Co. actually ran the Indian colonies as if it were a colonial power on its own. It had its own military, etc. I foresee these earlier corporations or "joint stock companies" would just turn Fur, Spice, Ivory, silk into gold. There could also be a Dole fruit company to exploit bananas. In short every resource should have the ability to be exploited by some kind of corporation.
I'd also like to see certain, highly promoted units to get some special powers. Right now the first unit to get to a certain experience level opens up the possibility to build the pentagon and west point. I'd like to see those kinds of units get a special designation, and be able to go home, tour the home cities, and by doing so reduce war-wariness. I'd also like more detail along those lines: a naval as well as a military academy, and in addition an air academy, a cavalry and artillery academy. Great Admirals and Air Marshals, too.
Right now after a unit gets so much experience, the player is given a choice of promotions. I'd rather have those immediate promotions limited to experiences the unit actually had: If they ever attacked from a ship or over a river, they are allowed the Amphibious promotion, If they defended in a forested hill, the promotion options would include Guerilla and woodsman. If they healed entirely in the field, the player would be given the option to choose the medic promotion. Once a unit earned promotions, players would have the option of bringing the units home again and attaching it to a barracks. The barracks would function much like the school/college/University did in Colonization. Subsequent units built in the city of that barracks would be allowed only those promotions made available by the attached units. All promotions would have to be learned 'the hard way' (in the field) the first time. The teaching units can also be 'detached' from the barracks and made active again, or moved to another barracks. Returning them to active duty would be less and less practical as technology progresses. This proposed process would also mimic how good officers and NCOs are deployed as instructors as they get older. The current restrictions on which unit could learn what would be lesser (riflemen could get the city raider promotion, if a unit with that promotion were attached to a barracks as trainers.) The basic barracks would hold one training unit, but city and national improvements like the pentagon or a Naval academy would open up extra slots.
In general, I'd like to see a much more detailed and complex system of unit promotion that depends more on making use of experienced units.