I realize this risks turning this into a suggestion thread, but maybe tie it in with a variety of bridge modules?
No bridge (Fighter, FAC) gets you a ship either with a single commander or none at all, depending on how in depth Steve wants to be. I'd actually suggest none, since having to assign commanders to hundreds of fighter craft always made me wonder if anyone played without automatic assignments on.
Then there could be the normal 1HS bridge, allowing for a commander, a 5 HS science/tactical/engineering/command bridge allowing for a science/tac/engineering officer or CAG, things like that, and maybe boost the flag bridge up to 25HS and have it allow for all of those and a task force command. Would add some more personality to ships as well.
On the point of "no commanders for fighters", you know there is a Fighter Combat Bonus on commanders for a reason, right?
Both that and fleet initiative rating is -very- important for fighter combat, I figure, as high-speed interception can make the range- setting for each engagement more significant.
Also, given how promotions currently work (you need 3-4 commanders in an immediately subordinate position for every single commander promoted up into the next), you'll need a lot of ships to compliment them anyway.
Also provides the opportunity to get your "ace pilot" with the impressively high Fighter Combat Bonus and fleet initiative rating to make fighter battles a bit more exciting, as they currently are.