The game set will be in a real time. Building a large city from scratch takes decades. So it will not be possible in SE.
Wait a minute, didn't you say that you wanted nanotechnology to be part of humanity's technological capabilities? If the player announces that a planet is suitable for colonization (And you said that communications would be instantaneous. Quantum entanglement? Do you want to use the word "ansible"
?), AI-controlled colony ships could arrive in large numbers and start using nanotech to grow buildings.
It also occurs to me that if we wanted to exploit resources on planets, using nanotechnology to assist with mining would be a more realistic gameplay mechanic than finding everything you need lying on the surface or in shallow caves, like in No Man's Sky.