Do you like the idea of adding an option that limits the availability of natural resources?
When this option is enabled, it is no longer guaranteed that each city will have a deposit of every type of natural resource.
For example, in a game with 5 cities, only 2 of them will have iron deposits in the beginning of the game with new deposit sites being added randomly in different cities from time to time.
The option can be either added to the new game settings menu or added to the script system.