TheLopez:
Distance from the capital city relative to the size of the world would be most important, but other potential modifiers might be being next to the ocean, or being on a different continent. An American example:
The first city founded (in my mod) is New York. The second city gets founded close to the first, and gets named Boston. The player then decides to start a city far away from the capital, say, a quarter of the world? - maybe there's horses - and it gets called Los Angeles. They then decide to fill in the gap between the two cities with one a medium distance away, and that's Chicago. Finally, the player spots an island and founds a city (colony) on that - Honolulu.
Is this something theoretically possible?
Another, far simpler script alteration would be to have city names dependent on the leader instead of the country. Washington would have a first four cities of Boston, Philly, NY and Savannah, where Roosevelt would start with NY, LA, Chicago and SF. (This would be especially useful when Stalin shows up)
Finally, while I'm getting excited about potential things to do, cities could be renamed according to civs! Apparently this is quite possible, at least in one of the mods the game shipped with, when Rome took over certain Greek cities, the names would change to the Latin version. Obvious example is Byzantium becoming Constantinople becoming Istanbul.
I can see that one getting very complex, though - if the Romans, Greeks, and Turks are all in a game, then the first one to found their version of the city should stop the others from founding theirs.