I don't know about uninhabited. What's written is that the habitable planets had been inhabited before before the gate to the sector was cut off and everything gradually went into the toilet. I know that there are certainly going to be planets that people could settle on as there was mention of people going a bit wild once everything was well and gone. You might have to defend the settlement from those wild humans here and there, but it's not like you're going to have to defend a small outpost from states that exist on the planets nor anything beyond bows and arrows from what I understand.
As for colonies themselves, I think Alex claimed somewhere that the player wouldn't have the ability to colonize in the game. The reasons he gives for this is that at the time of starfarer, everything technologically related is on the decline. People are able to maintain and construct cruder tools that do the job more or less, but the high technology stuff the sector had when it was in contact with earth is no longer possible to produce. As such, it's going to be quite hard to ferry over hundred or even just tens of thousands of people onto a planet, and this is assuming the player has the ability to convince the people to go there willingly.
The second reason has a little to do with the first. Inhabited planets are going to be massive power houses compared to stations and such due to their sheer population. Perhaps planting sever thousand people on a planet might not be all that hard, but given the story's restraints, they might not be able to successfully get the planet up and working anywhere near self sustaining levels never mind funding a fleet with resources, cash, and manpower for their ships.
For all intents and purposes, the player is in charge of a small fleet from what I could discern. Getting the cooperation of more than a few hundred thousand people is probably going to take a bit more than that.
Maybe we can establish outposts on moons and asteroids though.
