There are reasons why civilization takes time to rebuild in the world; why people fear to gather in settlements and stick to small, often semi-nomadic groups.
Sure, it is hard to find sufficient nourishment from the land - the first requirement to have a permanent civilization. But there is a darker reason as well...
Five people in a tent are invisible to the many threats of the world. As long as they don't go into spider-infested woods, and are prepared to move far as soon as one of their goats is found torn to shreds come the morning, they can survive.
A settlement of a hundred people with a stockade can hold off a darkling raid, but is beneath the notice of some of the scarier monsters out there. A dragon would not demean itself with demanding tribute from it, for what can they offer.
A city, though, big and gleaming, with tall spires and wealthy merchants - now that is a prize that many intelligent monsters would dream of plundering. The monsters remember a time when humans ruled the land, and they don't want that back - if the humans start to band, the monsters will disperse them by force. And the humans know that too, and are afraid of the bigger cities.
[Game mechanics]
Essentially, each city size level should apply a prestige penalty to the city, affecting the rate at which it attracts new inhabitants.
This should be probably go something like (2 less at size 2, 4 less at size 3, 8 less at size 4, 10 less at size 5). Minimum of zero - emigration does not need to happen!
This makes for an interesting mechanics - large cities can be made to use food more effectively (as they have access to buildings which provide more people per 1 food), but require additional prestige-generating buildings for full effectiveness.
Building bigger cities will then require further research and production to build the appropriate buildings that generate prestige, and so overcome the penalties. Additional prestige-generating buildings can be added to beef out the Diplomacy tech tree (Opera, Parliament) to help out. City walls and other defensive improvements can also have positive influence on city prestige.
Conversely, the kingdom can choose to be spread out over more, smaller cities, which will not be as efficient in food usage as the built up ones, but will hopefully cover more resources. Initially, such an expansion strategy will result in a bunch of small, level-2 towns, with small influence radii - a perfect representation of a fantasy kingdom with small pockets of civilization separated by stretches of wilderness.
