Something about roleplaying... and a furry...
Hmm. As to the shared-control thing, you couldn't have it on the same ship, but what you might be able to do is have a modular ship in multiplayer and some FRED commands. Hence, when, say, the engineering "section" (really an independent ship, permanently docked to the other components from the beginning in FRED) gets a bunkerbuster in the tail or loses power due to a pre-scripted event, you can have the dude playing engineer use a walkie-talkie to inform the guy playing captain, hit a button setting off an alert, whatever. It'd take about a thou in hardware to set up, but you roleplayers seem to be rolling in it anyway so there you go. Or you could even automate it- set up the play-captain's room with multiple monitors giving displays from the different computers (a lot of wiring and probably even more money, as well as some tech savvy), and throw in some FRED codes so that the appropriate people at the appropriate times.
I think it goes without saying that turrets are another story altogether, though you could potentially knock together a few ball turrets if you don't plan on having the ship, say, move. THAT could ge ugly REAL fast.
As for docking, set a special explosion. Kill those suckers when they get to the dock bay and press a button, be sure to disable comms first. Then all you've got to worry about is getting them back in the game.
And the, ah, "commander" can change mission parameters the same sort of way. Set up the game with some sexps so that certain keypresses can change certain objectives or send certain messages- or set up options, with y/n responses. Simple enough, same sort of **** I did as a newbie working on LB.
As for external, again, easy. Have an invisible, invincible ship with no weapons and maybe no engine control. Set it about 20k out, and tracking the freighter.