Originally posted by MxM
How about this:
The colonies should work exactly the same way as they are right now, expect that they have borders the same as the basic town (3x3). Similar like small cities, the colonies can be culturally converted (they have 0 culture).
However in future, if you want to upgrade the colony into a city, then you have to use SETTLER to plant city on top of it, or in one of the nearest tiles. In this case the colony would disappear, or become some tile improvement, depending on the recourse (e.g. mine for iron). Whatever.
The main idea is the need of the settler to convert a colony into a city, and giving borders to the colony, the same as for the smallest city.
As for ports and airports, I think this can be improvements build by worker on the tiles. As long as the colony is connected by road to port or airport, the colony will use it. Actually I think it is may be more realistic this way - quite often initially ports are separated from the place where the resource is collected.