Why not limit the number of cities you can found based on the amount of food you generate? The more food you generate, the more cities you can support. Each city requires more food than the previous one.
Once connected to your trade network extra growth of your cities could even be centrally regulated by distributing any empire wide food surplus. This way you could specialize some cities as agricultural centers of your empire.
And as food is a resource you have to produce yourself, your strategic choices would not be limited by where some luxury goods are located.