I am planning for a fantasy scenario (yeah... well I just got to test it), in this scenario every city will have it's own unique units and it's own income of food (which actually will represent money). I don't think I can do unique cities directly (correct me if I am wrong), but if i make a unique city improvements for those cities that have unique abilities then the abilities could be connected to the city improvements instead. These city improvements shouldn't be buildable and they shouldn't be destroyable and they should exist in the cities where they are at the start of the scenario.
I tried to load a ruleset I've made with 80 unique buidlings (first time I tried and I didn't know about the analyse feature) and it seemed liked it crashed but maybe I should just have clicked through 80 warnings.