Interesting... alternative ways out of the solar system would give interesting options: No jump points? Not a problem.
As for my input, well, others have already pointed out that there needs to be more CIWSs. I think 5 would be a bare minimum - 1 CIWS per 1 million of tonnage. On the other hand... You could increase armor. Armor may not be necessary for stations, the ones that can be salvaged by a salvage ship anyway, but going into the unknown? You might want to give the ship a bit higher survivability.
Remind me folks, shields are a military system?
DeMatt gave good points. Mostly about recreation and ground force transport facilities. Though, you could add a ground force transport ship separately. Maybe a colony ship as well, allowing the Unity to function purely as a habitat? Or, add a seperate Orbital habitat station?
Survey ship is already included...
Perhaps Unity would be better off used as a component/ship hauler across the stars, rather than have-it-all in 1? Since you still have a separate survey ship, I think you don't need that many different command and control systems.
Should tugs - ships with a tractor beam - be included? It may not be necessary since Unity can carry a lot already, but... just in case?
Any terraforming modules or separate terraforming stations? Or do you plan on building the stuff at the new world?
I guess that with these changes, Unity could be reclassified as a mothership
and renamed into the Pride of Earth Anyone played Homeworld and/or Homeworld 2?