Oddly enough, I was thinking about something like that for a mission that takes place in a campaign I'm considering FREDding. I had intended it to be split into 2 missions with Red-Alert joining the two together, with the first being an attack on a cap-ship group, while the second part is protecting one of the cap-ships you captured while engineers get its engines repaired. The first part would require more heavy weaponry, while the second part needs more anti fighter and bomber weaponry. The idea I just had would be to script in the arrival of several support ships right near the end of the first part, each ordered to dock to a fighter. One will dock with you, which triggers the end-mission sexp. I think there's a way to elimitate the debriefing and go straight to the next mission. There, you'd have the option of changing your loadout. The mission starts with the support ships still docked, and perhaps even performing hull repairs. The support ships then undock and fly off into subspace, and any other support ships the player calls on would be the normal type that just repair and reload. I'm not sure if this all makes sense, but there it is.
Later!