Right now, fighter pilots are treated as disposable. Does anyone ever take recovery shuttles, except for RP purposes? From a gameplay perspective, you're incentivized to just pick up more crew when you run low. There's no reason to try to save pilot's lives.
Contrast with marines, where your elite marines are a precious resource and players don't want to squander them. You actually care about marine losses, because replacing them with novice marines is a big deal. Keeping your experienced marines alive feels like an investment.
I think there's a huge design space open here to make players care about their fighters more. If pilots were a resource that gained experience and became elite over time, players would feel more invested in their carriers. Perhaps pilots ought to be a separate category, like marines, instead of drawing from general crew? It would make sense : A pilot has to be highly trained, and the difference between a novice pilot and an elite pilot SHOULD feel like a big gap.
Having a fleet with elite pilots, the player should want to invest in skills and mods that reduce pilot losses. It also could affect gameplay a lot: Do I want to accept potentially higher losses of throwing elite bomber squadrons against REDACTED or a star fortress? Maybe I want to invest in more expensive, heavily shielded fighters so my elite pilots will last longer, even if it costs more OP / potentially deals less damage? Or I could RP that the sector is just a harsh, deadly place and my pilots will die a lot, but at least now there's a tradeoff where I'll never have elite pilots. The decision space would be really interesting imho.