My thought's on the missions is that some of them should be multi-threaded.
Sure we should have the standard missions we have now, but there should also be some randomly generated "quest" type missions that take the player through multiple systems and dangers.
An example of one such mission could be: You pick up a seemingly innocent cargo mission from Wolf 359 to drop off Biowaste at Duamta. En-route you get interdicted (or a message) by an AI who tells you that he's only here to warn you that the cargo you're carrying contains something (either something very dangerous, or something very valuable) and that you should meet up with him at a station in the Saktsak system where he'll tell you more. You travel to the station, activate the contacts menu and then get more information about who this guy is and who he's working for. The information he gives you is that he's part of a galactic intelligence agency and he now wants you to take the cargo a to location in deep space in the Stopover system (the locations would be random, and could even be the rings of a gas giant or the orbit of a planet, or even the surface later on hen we have the ability). You travel to the Stopover system and are almost immediately interdicted by a ship or ships from a rival faction (the people that set up the original cargo drop mission), they say that you have a choice of dumping the cargo or dying (you could also try to escape). If you dump the cargo, then the faction the original contact works for will not be pleased and you'll lose rep (they may even turn hostile), if you escape, or fight back, then the rival faction will turn hostile. Upon reaching the fleet with the cargo you find a small skirmish with some enemy fighters attacking the other ships. When the battle is over, you are instructed to drop the cargo and you're told to dock at a nearby station for your reward (or one of the ships could drop containers of credits, a large amount, as your reward).
Of course, the mission wasn't mandatory and you could have avoided all this if you'd escaped the first interdiction and just gone to your original destination in the first place.