Another possibility that I suggested in another thread is:
Each square has a certain quantity available to it for workers (i.e. 1 through maybe 4 or so). You can assign workers to the same square up to its limit. This would allow that a very fertile region (think Eastern U.S. seaboard, much of Europe) could be created with cities right next to each other and still allow those cities to be productive. This would be especially true if the more accurate factor in determining city size (i.e. the availability of fresh water) were used to limit the size in the city. You do this by assigning food to flow to the cities that do not support themselves.
Thus, you could have Boston, NY, Philadelphia, Baltimore, Washington, Richmond, Cincinati, Cleveland all on a world map where they historically actually exist. Meanwhile, St. Louis and Chicago might have squares being worked that provide lots of extra food that is being shipped to the above cities.