One thing would be great is to have smaller recon fleets consisting of 4-5 ships, who recon their specific faction's sector. Also it would be great to have some "ship class staircase"system.
For instance:
If specific faction has at least 3 stations present in the sector, Cruiser(and above) class ships may spawn into the sector for defense.
This would enable us to amass large ships into a sector for hire, and thus have a strong fleet for offense, to take over nearby systems.
OH, and something else hit my mind.
I'm not sure about how Shipyards will work, but i do have an image in my head.
They would act like factories, for sure. You can give them resources,or credits ,so they can build ships to hold the sector. The ship built depends on the amount of resources or credits the shipyard posesses. Also, if you have enough credits, you can order the shipyard to build one of your ship designs. These ships will automatically be assigned to your fleet upon completion.