Its a personal choice. What I tend to do is have 2 pilots as Player Characters (PC) who you fly , and the rest are NPC (non player characters) who you fly using AI solo rules. for any mission you choose if you want a PC to fly or have all the flight NPC just as you would if you were CO of the Squadron. If a pilot is wounded he is grounded for whatever time the the dice role dictated. Thus a pilot out for 2 missions is deemed not on the slate for a sortie. until he has been seen by the MO declared fit for duty. 2 missions after his wounds/crash.
Thing is to make it fun and to reflect the fact you will lose NPC and PC pilots in the campaign, but hey thats what makes every sortie different. Would you risk your PC pilot in a final swoop on a fighter or retire to fight another day ???
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