Steal this from Zeus/other city builders. A nicer building gives you a lot fewer of a more valuable population -- nobles, scribes whatever -- that get used to maintain more valuable buildings. Specialist pops should also be a LOCAL resource -- as in, having them in one city does not allow them to support buildings in another city! For city leveling purposes, have them count for multiples of standard pops.
Creates a clear alternative to city spam, makes specialization more interesting and less about spamming hordes of workshops etc, and makes cities more fun to build.
As an example:
City Square: 4 squares, level 3 city, enables high end housing for the city
Dormitory: 4 squares, 5 scribes, 1 food
University: 4 squares, 20 scribes, generates 40 tech research.
Arcane University: 4 squares, 20 scribes, generates 40 arcane research
Villa: 4 squares, 5 nobles, 1 food
Command Post: 4 squares, 1 noble, allows unit group creation
Training field: 4 squares, 1 noble, allows more experienced units