Though i mentioned this in another thread I think that the ideas section is a better place for it than sinking in a slightly related thread.
The Problem:
City spam seems to have a lot of supporters as well as lot lot of people who hate it. Honestly I don't think there is any issue with allowing players to dot the map with small cities, but there should be benefits to choosing to spam cities as well as in choosing not to do so. Currently you may as well drop a city any time you see something you like and every time you see a forest, as well as every time you take a breath as every city is just free wealth. Unfortunately adding mechanics to the game to restrict city spamming will just anger tons of players who enjoy that play style, while not doing something about it angers those who don't like being forced to manage tons of cities. Even if people didn't mind a change I think it would be rather counter productive to use game mechanics to force people to a specific strategy.
An Easy Fix:
Directly connect the output of resource nodes to the level of the city it is linked to, and or, to the population of the linked city. This would allow players who enjoy spamming cities to spend their food on many small settlements with lower production level nodes while players who prefer to have a few cities carefully placed near groups of nodes could level those cities up with their food and gain similar income benefits without being forced into a play style which they find distasteful. The one major issue I see with this plan is that currently food is more or less unlimited. For this to work caravans would need to be unable to generate food. It is rather silly that caravans magically make food as they travel and removing this inexplicable power would make people care a lot more about food nodes (which are currently pointless after the very early game). As the game is now as long as you get 1 or 2 on a city you never need to worry about food again as you will have hundreds of extra food (or at least I did the time or two I played that way).