Some further ideas:
More types of missions seems to be an obvious one. The current missions are all fighting missions, which makes the game a bit irritating for the trade-type player. Having missions like ... well, Railroad Tycoon
... would help a bit: fast shipments of pharmaceuticals and oxygen to a base hit by terrorist attacks, steel or alloys to rebuild Freeport 7, ...., and perhaps some Bretonian beer to complement the awful Liberty ale on Manhattan when a diplomatic mission from Bretonia is coming ... The fight missions could (it seems) easily be complemented by wingman mission/freight protector missions, exactly on the pattern of Mission 1 of the story.
I think some kind of improved navigation computer would be useful: one that
does take newly discovered routes and jump holes into account. A trade computer that made it easier to see who sells and buys what would also prove ueseful: at present it's paper and pen that rules. (Or at least an cut and paste interface to Excel...)
I can image a number of mission types around building new trade lanes -- moving material to waypoints, guarding it until the construction fleet has arrived, etc. And perhaps blasting asteroids to leave place for a trade lane (though collision physics seems not to be important in these...).
Scouting missions have also been mentioned. These would probably require some thoughts about how the scanner device really works. It seems a little too easy
to pick up readings when you're going by trade lane, for instance...
A thing I'd be happy to see gone are some very-NPC things: I once tacked onto a freight convoy just to see where it was going and how (one way of discovering jump holes), and found that it moved gold from Manhattan to Norfolk Shipyard. (No gold at either place that I knew of, and as far as I could make out it just shuttled to and fro with the same cargo... didn't make sense...). And every time I exit from Trenton Outpost, three Bounty Hunter Pirhanas go past ... every time...