ok, let's start dreaming...

a new knossos is found, the new GTD Kickass with many support ships pass through it, but then the knossos explode and the node collapse. You have to make your way to home, you are in an unknown region surrounded by shivans, with limited resources.
The Kickass has some autorepairing systems, some support ships can be converted to factories, but they all require resources; you can convert some transports into mining ships to collect plasma from nebulaes and metals from asteroids, you can try to stole ships and resources to shivans. And you also have some science vessels, that will be converted in order to develop new technologies.
During the missions it will be often necessary to protect the mining ships (or you gain less resources), the factories (or there will be a production slowdown of new ships), the science vessels (or it will take more to develop new technologies).
The system is adapted to your strategies: if you often use bombers, more bombers will be built, and there will be more tech advancements for the bombers (not necessarily new ships, new stats too). If you choose often torpedoes, more powerful torpedoes will be developed, if you call in, as reinforcementes specific ship types ( awacs, interceptor wings, etc) there will be upgrades in this direction, in order to have more ships of this type, and more advanced.
Succesfull contacts with new species, ancient artifacts studyed, enemy ships captured may cause tech advancements.
The idea is to define some variables, like *bombers* *interceptor*.... *torpedoes* *fireforgetmissles*... *techadvancements*..*resources*... and many others, and assign them a value after each mission, depending by what happened, and use those values to define the loadout. It would be cool to have a random number generator, but it would be also possible to use some predefined levels (example: if value *bombers* is > of 20, then faster bombers will be avaiable, if value is >60, the bomber type XXX will be aviable...etc etc)
Persisten variables could also be cool to define the AI level of your wings... if a wingmen survive, in the next mission he will be stronger..etc etc
Well, this is a campaign I'd really like to play:)
damn I need to start learning FREDding, one day or the other:p