I have been having similar frustrations with skills to those I have seen others talking about--I feel compelled to spend my points on fleet skills, and then find that I am sometimes best off delegating command of my highest-impact ships to officers with skills to get more out of them. (Particularly likely if your best ships are carriers.)
I propose allowing players to assign an AI officer to their flagship as "flag captain", providing his bonuses (and possibly his personality to autopilot behavior), and allowing the player to take campaign skills and still pilot whichever ship he prefers.
The big negative I can see is that it makes taking combat skills on the PC himself even less attractive (although not completely pointless, as using a flag captain uses an officer who could also be piloting his own ship).