Why not have food transport effectiveness be the inverse of city level? So, say you've got a level 5 city, and three level 1 cities, all hooked together. The 5 transports at 10% efficiency, while all the level 1s transport at 50% efficiency. 

The idea being that higher level (and thus larger) cities consume more of the food they grow and generally dedicate a smaller percentage of total resources to agriculture, while lower level (and thus smaller) cities are more agriculturally based. 

The player would then be able to choose between either having a few megalopolises and a large number of hamlets, or having a bunch of average sized cities. 

Having higher food transfer efficiency at lower levels would also be a boon for the early game -- cities would grow quickly thanks to lots of food aid in the early game, while in the mid game the higher absolute sizes would be balanced by lower population replacement capability -- in effect mimicking the demographic trends of the real world.