BoogieBac, a thought. From my limited (2 days) playing time, I've been razing parts of the city as I upgrade. When I build a Marketplace (6 gold, 4 spaces), I raze all Merchants (1 gold, 1 space). Now, how about allowing the Merchants to upgrade once a city has a Marketplace? They still produce 1 gold, but could also specialize, based on any special resources near the city. Or perhaps allow us to choose from a list, per Merchant. This would add variability to the cities, and give us a reason to hang onto the 'minor' upgrades once we get the newer ones. (EDIT: I mean, specialize in a type of uncommon merchant goods to carry, such as potions, etc).
A similar mechanic could be used for Studies - once a School is built, perhaps the Study could specialize in a certain type of research. Perhaps it would give 1 generic research point, and an addition +1 in a given tree, when that tree is researched. Again, choose from a list based on what is built in the city. If there is a minimum of military structures, then the Study could be upgraded to give 1 general + 1 military research.