villages would be connected by transit and walking paths.
How do you connect them all most efficiently?
Perhaps concentric rings, with a special hub-town in the center
Transportation
You have subway lines underground, connecting the villages, first a continual, straight line, then connecting to a central hub for a hub & spoke design.
subways have cars for people and cars for cargo. (to accommodate automated cargo-pods one day)
4 stations per spoke means 6 villages per hub, or 1500 residents per station
a large central station under the central hub where people moving between spokes could switch between lines or hop onto transport to the seaport, airport and roadport.
the spokes and subway lines could be named for their cardinal directions: N, NE, E, SE, S, etc
between the villages and stations is empty greenspace.
a ring of greenhouses form a wheel outside the spokes, perhaps.
central hub would also contain
an endpoint for transportation to the port.
underground parking for cars, which is the endpoint the car/truck road to the city.
storage facilities for goods entering & exiting the city.