Salvage operations
Alien invasions
Rescue
Search and Destroy (with a hint)
Bounty (aka JSteiner Azek J1 UIT mission) :)
System defense

Have any more? Suggest em!

The 7 samurai mission!

A small, out of the way mining outpost hires 7 players to protect them from an approaching army of bandits!

Two suggestions the first one is similar to the system defence suggestion above and the cargo capture mission already in game.

With the advent of mining there could be a resource war between factions and bots. The way I would see this being done is within each nation’s borders is a specific ore type, unique to that nation, all with the same properties, market value, etc. Points can then be awarded to the nation who collects the most ore of the one of the other nations (the same as the cargo capture missions). The attacking forces will be required hold the sector will miners do there work. I'm not sure how the UIT will fit into this scenario, as they will be required to attack and defend from both Serco and Itani. Which may affect their neutrality status.

The second suggestion is a mission to clear all the bots from a sector. This mission will spawn bots in an empty sector that will need to be destroyed. These missions could be graded for new players (collector bots), experienced plays (hive bots) and groups (multiple hive bots, maybe even a cap ship in time). Variants of this mission will be to have the bots roam from sector to sector so the player will need to hunt them down. Maybe, with either being given a specific flight of the bots or a multi-sector scanner that could track them a few sectors away.

Thought of some more:

Participating in strike forces
Trade companies
Escape missions, ie run from awesome and superior forces in a wimpy ship