For one, you could give the system more structure, like you said, have a central planet that the space revolves around (both literally and...the other way).
Another thing you could have, is space stations, where you can dock and live in peace for a bit (and design/upgrade your ship). From the space station concept, you could have 2 factions form, pirates and the police. If you get a bad reputation with the cops, you can't dock at space stations, and cops around space stations try to kill you. On the other hand, being in good rep with the pirates could make other pirates less likely to attack you, granting you peace and calm in which to design your ship as well.

And then even you could have missions at space stations, like convoy escorts etc.

I don't know how complex you want to make the game, so I just had this spurt of ideas. If you're aiming for Cpt. Forever or similar, I guess some of them might be a tad too complex...

(Captain Forever just wasted me half an hour of my life...)

P.