This'd be cool, problem is that FS campaigns do not work as a single unit. They're a lot of missions strung together and played in sequence, with no correlation between them but that which can be synthesized in FRED (and, yeah, Red Alert missions). All these other games, you keep ship and environment information from mission to mission, and the campaign acts as a unit. That means if you have X number of rockets in the hangar at the end of the previous mission, you can carry them over to next time, and if you disable and capture a ship, you can take it into the next mission with you.
That doesn't mean a lot, until you realize that that means that virtually everything not the engine would have to be replaced. Continuity would be awesome, but I don't see it happening quite so soon as, say, Newtonian physics, voxel support, and a 40000 poly-per-ship limit. In other words, don't hold your breath.
Besides which, there are other problems with it, such as the inevitability that people will try to do this with ships not meant to be human-piloted. You can fake it in FRED for now, but that's as far as you're likely to get for a while.