Spacestations

I like the general idea though you're light on detail. Space station could be used as a way to mark a territory as yours without colonizing it.  They could have additional offense and are destroyable like any ship, just a large one.  They need steady supply of food, money (costs money to have a space station but that isn't just taken out of your wallet but moved to the station) need ships taking people/manpower back and forth (which can be intercepted which will make the people unhappy) and when in production, ships going back and forth taking production to and from a system and the station are needed.

Stations can store ships, upgrade ships, repair ships, claim nebulaes for their reward. Guard areas just like any fleet with the same effects. Nothing to stop you from building a space station in your own systems (in case no supply chain needed but a enemy fleet can still barracade supply and still need those resources regardless) If you have peace or alliance with another faction you can allow them use of your space stations with a fee for use. 

Space stations produce nothing, or maybe just some influance based on number of ships there. But they don't add to system unhappiness, even if in a system you haven't colonized.