For the trader missions i think it's not that hard, if you can switch out enemy fighters for caps, the you can do the same but with enemy containers.....and this is not my idea.....i just remember......so it's simple
-Go to "X" system there is our big bad enemy's supply depot or hell know what else.
-Shoot out the containers.
-Pick up the stuff. (big one what takes up a lots of cargo maybe 500 or more)
-Come back, and give us what you found.
-Profit.
Longer trips can give some work for escort if they're in the right place in the right time.
I think patrol mission are also can be done, we have missions with more than one waypoints. Increase the number of these waypoints and make enemy encounters attached to a percentage. I don't know if it is possible or not.
For cargoship hunting it can maybe done like this: one transport with GB and fighter/bomber escorts *here comes the le switch ships magic*. I'm sure all you know this situation...you shoot down half of the hostile fleet and they start to flee to another waypoint. This can be used in this kind of missions too. You go there and find the trader ship and its guards, they start fleeing to another waypoint where heavy weap platfroms and other nice things waiting for the player. If they can stop and take out the convoy at half way, the're lucky if not, then it's time to prepare to the hard work.
I don't know how to create those missions, so maybe this wall'o'text worth nothing...but who knows.....
I plan to make custom missions at some point, but don't expect it prior to 4.88. Convoy missions will be possible (and relatively easy to create). I'm also trying to figure out how to set up a courier mission, but I expect this to take me quite some time. The way missions are set up on Freelancer is very chaotic and difficult to understand. Sloppy coding.
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I always figured mission against the Wilde, both of Rheinland and Kusari, off of bases in the Sigma's 13 and 19 for Kusari and various bases in Rheinland.
Missions against Nomads in the Omicrons would be interesting as well sponsored by Corsairs, The Order and Bounty Hunters.