Back when I was contemplating the Recon Campaign, I think my primary conceit was not so much the stealth mission, because few of the missions would have been purely recon, but rather a Crysis-like stealth mechanic to let you disappear and having various "levels" of stealth. Your stealth fighter would have an option to kill your weapons and burners to "go dark" where you wouldn't be detectable from more a hundred meters or so. With everything active you'd still be stealthy, but more detectable, and when you started shooting you'd be visible until you went dark again.
Part of the problem I had in the end was trying to properly incentivize the use of the stealth aspect. Setting and resetting visibility and enemy AI patterns that much drove me insane, and I never fully worked out how to do it best. At the end I was toying with some kind of idea about sufficient damage compromising your fighter's stealth too.