This is, of course, just the opinion of a FRED noob that is only just starting out (and I'm sure someone has already covered this idea here), but why couldn't this be done by using several 'jump nodes' leading to different objectives? They could be made conditional, so that you couldn't use certain nodes until others (in or out of order. by the individual player's choice) had been completed.
The base could be, say, a decommed destroyer (a la that Orion in Transcend in the asteroid field, or the Typhon with the docking ring in Derelict) or some such. Docking with it could be your resupply/repair/choose a different ship and loadout point.
I'm sure someone else has already thought of these, of course, but they seemed like ideas worth voicing anyway. I certainly don't envy the sheer amount of SEXP scripting and debugging the designer has to go through for all of that...makes my head hurt just thinking of it.
But it does have a lot of potential. If anyone does come out with a campaign in this vein, I'd be happy to playtest it.
I did exactly this a few years ago as a proof-of-concept:
http://staff.hard-light.net/goober5000/downloads/freespacelancer.zipSo far I think there have only been two attempts (Mercenaries and BHX) to turn this sort of concept into a full-fledged campaign, but neither of them were ever completed.
