Short term I think the easiest way to do "truck" stops would be to allow colonies to sell fuel, in the same way the pirate bases do, although probably for more money. Of course not all (or possibly none?) of the colonies are known to the merchants at the start of the game, so as the player sells knowledge of the colonies to the corporations the routes might have to be re-calculated. This is probably too processor intensive though.
In the long term the introduction of more entities is going to require some fundamental questions about how the game universe operates. Right now we're in a sector full of ancient ruins which are being exploited by 3 mega corporations. There are merchants who trade between the corps, pirates of prey on the merchants and pirate hunters(mostly corporate) who prey on the pirates. This whole setup is fueled by the bunches of cyberneticaly engineered mercenaries who fetishize alien artifacts and walk around surrounded by cheerful octopi (I am of course referring to the eponymous prospectors). In this setting independent "truck stops" don't really make sense (why wouldn't they be bought out by the mega corps? How are they really different from the space stations?).
Magellan has already mentioned that he is adding in much more active, ftl capable, aliens. It seems like this might be a good time to expand the "universe" a bit. By shrinking the current game rectangle down to say 1/2 is current size and calling it "human" space, where most of the stars position are known, if not freely available, and there is a strong corporate presence. There might still be some pirate fleets here hiding in gas clouds and anomalies, but not many. Outside of this rectangle there would be eight other rectangles arranged around it. These would be full of pirates, aliens and independent colonies. Most of the real money in the game would be earned by venturing out of corporate controlled areas. Either via exploration, trading between the tiny colonies or fighting/stealing from all comers. In this setup it would make sense for there to be merchant owned "truck stops" away from the corporate influence. Some might even let pirates dock. All of this will move the game away from the mining and exploration and into meeting new races, finding cool crap and navigating among slightly less monolithic power structures. I think this outcome will make the game a little happier (It's really rather dark right now).