I usually ignore these systems as well; it's just too impractical to purpose-design ships to cross these vast gulfs between the stars, and distance restrictions mean that these systems will be cut off from civilian development.
Actually, a thought I just had is to make stars act like LPs. Since the AI movement algorithms now consider LPs for pathing, it should allow connectivity to be established within these tremendous star systems for players, civilians, and NPCs alike. I'm not sure if there would be other knock-on effects from doing something like that, since it's just an idle fancy, but it seems like it could work without requiring any alterations to the LP scripts.