It's pretty easy to come up with merc missions, but if I recall correctly there are only three merchant missions: Convoy, Transport, and Deliver. Here are ideas for a few others:
Mass Transport: You get to carry people in excess of the usual passenger limit (refugees, workers, whatever) to a new location. The game deletes most of them when you arrive, rather than distributing 50 people into a planet already. Killing anyone aboard results in a fine once the mission is expired.
Mercy Mission: Pick up specifically designed medicines from Acorn (always Acorn, just like you always go to Trou to drop off prisoners), and not only go to a given planet, but administer treatment to 1 or more peds in the environment. Could even be an excuse for making the peds hostile, so you have to subdue them, or use smoke grenades to prevent them from hitting you before you can give them the drug that will cure them. Could also introduce a syringe rifle. Killing the hostile results in a fine.
Confiscate Cargo: You alone or accompanied by a squadron subdue a target ship, then the player ship takes all the cargo on board, then delivers it to the authorities. So the ship must be EMPed in order to recover the cargo. Not sure if this would require different NPC behavior to prevent them from destroying the craft, but there could be a new gun that has an EMP like effect that these ships would automatically be equipped with. Cargo is replaceable, so if you happen to sell some of item X, you can still pick it up elsewhere and the authorities won't know the difference. Failure to complete this results in fines in addition to lost mission rewards.
Transport Hazardous Materials: There would be several types of materials that the player would have to move from one location to another as quickly as possible. The more time they spend off of an optimal route, the more the chance that things will break down and cause problems.
- Hazardous waste containers might leak, from weapon hits or over time, causing the player character's health to drop, or to gain injury status, have sight problems, etc.
- Xenomorph (or whatever joke you prefer) containment cages that if the ship is jostled with collisions or weapon strikes will cause them to break free and run through the ship trying to kill you.
- Mass Prisoner Transport, similar to the mass transport of civilians etc above, but a chance that one will break free, unlocking others' cuffs, giving you an on-board riot of sorts.
In addition to the cargo stuff above, thought of having emergent, ongoing bounty missions that are part of a bounty board at Loye, Haack, the capital, etc (and perhaps a pirate equivalent board for notable confeds, Kilrathi, retros). These are the ten most wanted, which the player may run into anywhere in the whole map.
There's no public expiration, but over time the chance increases that the NPC disappears for one reason or another, announced in the news as a capture, escape, turned self in, destruction etc. These would be non-hostile targets that have a very low tolerance, so bumping into them or accidentally shooting them will tip them into attack mode. They can then be avoided if you want, or taken if you think you're strong enough.
In-flight conversations include the possibility of hiring them, angering them, or tipping them off that they're on the wanted list, which will make them go into hiding etc (without you getting any bounty for it).
They have planned routes of travel, frequenting certain areas, so players who happen to run into them can maybe run into them later. If two plans happen to overlap, they will fight each other and one will win, the other will lose, which will also be announced in the news.