Finder of things, Doer of stuff
I think it was Wing Commander II that Ellen Guon had wanted to allow selecting your gender.
The easiest option would be to swap Blair and Angel and then edit some pronouns. I think you're only really going to run into trouble when Jazz attacks Angel and then flees... there you'd need to rewrite that scene and the following briefing (Jazz would attack you, then you'd tell the Major you were chasing him...)
The Blair/Minx kiss in Special Operations 2 would also be a problem, but it'd be outside the boundaries of the original challenge.
Art-wise I thought of that too... just swap one of the female pilots for Blair. However with WC2 you would also need to end up re-recording a bunch of dialogue - particularly in the intro - to allow for the gender change. There's a number of other voiced cutscenes as well IIRC. WC2 also has a couple of cutscenes that are an early animation format. The Blair/Angel kiss isn't an issue if those are the characters you are swapping. As far as I can tell the game just mirrors people depending on if they are on the left or right... I'm not sure if that presents any problems for Blair's different uniform in the WC2 intro or not. The other animation that would need art would be the takeoff/landing animations when the canopy opens/closes, but that's an issue for both WC1 and 2.