What did I like - the variety of the plot missions...
What was fun? - being a gunner, flying through an asteroid to spy on someone, rescuing people from bases etc. If those types of things could be incorporated, that would be terrific. Indeed, CLOSE SECTOR FLYING (ie asteroid, through base as fast as possible, through the city etc).
Most have been said, but some others
[Think] (or trade!?)
Prospecting mission... scan asteroids within a certain sector radius, with regards to a corp/miner starting up new operation or needing a new area for mobile mining possibilities. Obviously asteroids may harbour pirates and other low life, to make it more interesting.
[Think?]
Negotiate missions - from one base, they want something or some resource. You have to find a base that supplies said resource, speak to the boss on board (or person on board) and negotiate some form of deal for them. Alternatively, they are competative and have been marauding each other/sabotaging each other, and wish to stop this.
Options include insults as well as persuasion techniques, with possiblity of failing and succeeding dependant upon what you say. Obviously would need variety of options, otherwise would prove simply formulaic. Preferably some knowledge of how the races take comments etc to help win em over - ie "could go buy from boron/split/paranid then" - Teladi will be hostile to one or two, but compliant to one of the responses and agree to supply).
It may not be possible to create teh routes, but it would be variety.
[Think/Fight] (Pirate)
Negotiate with patrols of police (bribe if possible, options once more on when to bribe, too early - hostile, too late - hostile, just right = success) to allow a known criminal leave their airspace/allow a consignment of space weed through. Success will mean okay mission, failure will mean you have to fight (hostile) police/navy in area to allow bloke through. failure of fighting the police during mission (if incapable of bribe) = death.
[Think]
Open ended FIND SUZY mission, characters on some bases may hold information as to where she is... put it all together (after accepting mission at one base) - find her, get paid a handsome reward. Failure doesn't occur, if more than a few "days" pass, you fail automatically, but no negative rep etc. Once found, ship her home (cargo).
[Fight] (pirate)
Free the don! Engage military escort and personal carrier carrying a pirate don, once all escorts are down, and transport damaged... hail to get them to drop the don, whom you then pick up. Life support system needed

Time limit to mission once you attack, else help arrives for the military...