I'd like to see something similar to DLR and W4 sites, where a city can have any number of sites attached to it and its production or other attributes are then altered by those sites. For instance, a stables site gives all units produced in the relevant city +2 movement, a blacksmith site gives units +1 strength, a gold mine site gives +5 income, etc.
A site is a map object, occupies one square, can be razed and rebuilt, does not grant any combat bonus. Typically, only few cities on a map have one site attached, and very few have more than one. Furthermore, via map design sites should be placed simply near the target cities so that it's obvious which city has which site(s) attached without any additional interface work. By adding sites to cities, some cities can be more valuable and players need to think about conquering them early. As sites can be controlled (razed and rebuilt), they add a bit of strategical depth to the game. And... they are nice!
Just to be sure I'm well understood, sites are pre defined in a map, not generated at game time or whatever.