Realistically, the station should actually be the starting point of a player. One station per race (1 for zolarg, 1 for human,etc.) and after that you send space ships for every colony you start. I know it redefines all your idea x) but...
The station is orbiting around your mother colony (you can move it when you become independent?).
That way travel times could be introduced : 1 minute to travel from 0:0 to 0:1, 2 mins from 0:0 to 1:1 for example etc.
And also the more ressources you send the more it takes time.
Maybe some techs to accelerate the travel time (for end game colonies with lot of ressources), like researching better engines for the ships ...
When you buy on the GBT it can take time to get the resource, depending on the location of the other person's station.
When you post a trade on the GBT the ressources are sent to your station. All the resources you buy on the GBT have to transit by your station.
This will make players rely more on the commonwealth and the mother colony way more important (closer, less time to get the resources and if there is a starvation...) and rare resources that would only be produced by the zolarg for example will take time to come.
This would make the game more realistic, but much harder (maybe lower the civics costs for trades).
The galactic map would also become more important (quite useless right now).
The problem to solve is how you get the resources in your station to build ships to colonize planets...