But surely there are some cities on the map which are already the largest size (or will be reaching the largest size in a few years) at the start of the game? Rome, Carthage, Alexandria. Those cities all have their own characteristic layouts, which could make for some epic siege battles.

What would be the limitations of custom cities? Can you have rivers running through them like Rome? Can they be on the coast like Carthage? Or flanked by water on two sides, like Alexandria? Or do you need to be able to attack the city from all directions?

At any rate, the amount of effort required is just a matter of time and manpower. ;)