I think this came up earlier in the Part 1 thread - it's an interesting idea, but I think it'd make you feel forced to use ships with fighters just to make the most out of the bonuses. And that'd likely be the "optimal" way to go.
Perhaps the optimal method of catering to peeps who want more carrier/fighter oriented builds is to add a few more carrier hull mods rather than more carrier/fighter skills, whether or not such mods can be built in or not. IE, weaker carrier/fighter hull mods can be built-in, while the really powerful hull-mods cannot (like the upcoming changes for neural link and [redacted] ships can't be built in). Example of "powerful" hull mod: All fighter/bomber wings always launch with temporary Damper Fields (up to 3-5 "impacts" before going away, regardless of whether fighters have a shield or not), or maybe a launch catapult so that all fighters/bombers launch with a temporary speed bonus that lasts 30 seconds or something.
Point is that maybe having too many carrier ship skills runs into the same issue has having too many phase ship skills in skill tree... It wastes a skill point on a skill that might be better expressed as a hull mod. Food for thought. But I agree, carriers and fighters/bombers maybe need to have more varied effects that shouldn't necessarily be skill dependent, only money/OP dependent.
But then again, I keep complaining about bringing back fighter/bomber wing control to overhead tactical map so attack behavior isn't directed per parent carrier and that prolly ain't gonna happen, so not exactly holding my breath...