I don't quite understand why there is a big push for higher damaging cities.
IMO the model of siege warfare should be, defeat the opposing army in the field, set up your siege lines, bombard the city, assault the city. In this model, the city damage would play a pretty negligible role in the field battle, and during the siege the city damage would be minor. City damage being an abstraction for a raiding party/sallying force/archers on the walls, enough to be a nuisance but not enough to be serous threat to the siege. The strength of walls/castles being their ability make frontal assaults costly, therefore requiring siege equipment, therefore buying time for reinforcements to come lift the siege.
I think the proposals of: no walls = archer, walls = comp bow, castle = xbow is a good start. Cities should have a combat strength a good deal higher than contemporary melee units. Defensive buildings should add health. Blockades should deal damage to the city.