I don't know if this idea has come up before, as I only joined Apolyton yesterday.
If the tiles a city could use would be unlimited rather than having the maximum of 20, then more food could be produced by perfectionist societies.
I think a city should only be able to use the tiles adjacent to it, and then the ones adjacent to those, and then to those and so on. This would mean a small city of size four or less, MUST use the tiles adjacent to it (NE, N, NW, SE, S, SW, E, W) before being able to gain resources from the next layer of tiles (2 tiles from center), which would also need some form of infrastructure to have access. This could let size 50 cities have a larger than normal city radius, making them megalopolises. In this manner small cities cannot gain the resources which are quite a long way away from the city centre.
It would also make it a MUST to build at least some form of infrastructure. ICS cities will be made to work 'pathetic' tiles such as Glaciers and Tundra, forcing them to either change or improve the terrain. This would also lead to perfectionist Megalopis cities having vast amounts of goods and resources.
To further limit small cities, I think there should be a minimum size to build certain improvements and wonders. If a city had to be at least size 9 to build an ancient wonder, and even larger to build a renaisance or modern wonder, then ICS civilizations would lose all of their chances to grow faster. As I play in an ICS manner, I have found wonders such as the Pyramids and the Hanging Gardens useful.
In Civ II, an ICS nation, under fundamentalism, with Michaelangelo's Chapel, and JS Bach's Cathedral, gives an enormous source of money and happiness. I have found this incredibley useful to convert from a medium ICS to a massive perfectionist society. Fundamentalism MUST go!!! Once a player has achieved this in Civ II, they have won the game.
Large city solutions:
Production waste: I really like Korn469's concept of multiple build lines for improved cities. This removes the waste of production incured when building cheap things. Is'nt it annoying to build a barracks in a city which produces twice its cost every turn.
To many Elvises and Einsteins: Large cities often have unnecessarily large amounts of specialists, who often do unnecessary work. In my theorem above I have shown how large cities will be able to utilize more than twenty tiles.
Food Shortages: By giving large cities extra room, more food can be produced each turn.
Unhappiness: Large cities should have 'facility bonus happiness' in which each improvement gives one happiness, and each wonder gives 5 happiness. The scale for this should start around be 0 for ancient times, -15 for renaissance time -30 for modern times, and -45 for future ages. So that the improvement happiness equation is (age unhappiness+1 happiness per improvement +5 happiness per wonder)In this manner, unimproved cities become majorly unhappy in each new era.
Limiting improvement building in small cities by size would greatly limit selective building (I usually only build a Library and University in a city). This could be done by making the minimum sizes as such:
Ancient Improvement Size 3
Renaissance Improvement Size 9
Modern Improvement Size 27
Future Improvement Size 54
Wonders:
Ancient Wonder Size 9
Renaisance Wonder Size 27
Modern Wonder Size 54
Future Wonder Size 81
In this way small cities would have to be, at least in part, perfectionistic.