More thoughts....
Could missions be cued to ship types?
For example special missions for scouts? or for carriers? Perhaps even some special missions for freighters just in case a player might find himself stuck in one....
Maybe a mission like the training one on AOTK, but with a slight twist, have the pilot place in a Q ship in the middle of a convoy and have Orions attack the convoy. Only in friendly spce of course.
A run the gauntlet mission where you pick up a passenger or supplies from one friendly base and transport it to another on the other side of the map, of course multiple enemies start in between.
Mutiny, one of your races ships has mutinied and must be destroyed before reaching enemy space, this would give pilots the chance to fight vs their own or allied race ships for a change.
Time to get breakfast all this food for thought is making me hungry....