Ok someone must of said this before: I think when you upgrade or change to a different ship, the crew of that ship stay on it unless you choose to take the crew with you. That way if i want to take out a science ship (for example), or a ship designed to take on a enemy, you know that THAT crew has had its skills based round it.
Also it would be a good way to use up more of the crew that assigned to you, else, like with me, they just sit stale and never used. you could have it split even more, you crew for each ships plus a ground crew you wish to take with you, maybe one set with phasers, and another with polaron based weapons
I just feel like its a wasted, you spend lots of time building up an offer, only to get a very rare one which you want to use, and the only way to use them is if you get ride of someone fully trained up. plus it would give you a reason todo more of the old missions, to train your new crew up