Alex, how do you feel about me bringing up officer skills for carriers again? (I drafted a post some time back, but didn't submit it because meh)
Well, you're always welcome to bring stuff up! But as far as likelihood-of-me-doing-something, it's fairly low, though it depends on the specifics. I'm not a fan of bringing back carrier-only skills; the new skill system (for 0.95.1a) is a deliberate step away from skills locking the player into a too-small set of ships. Yeah, ballistic and energy masteries do that to some extent, but the range of interesting ships that these benefit is broad.
Carrier skills, there aren't that many interesting ships to pilot - Astral, Legion, Heron. Maybe the Odyssey. But combining carrier skill effects with non-carrier effects seems like it would still incentivize you to pilot a subset of these ships due to them benefitting from both the carrier and combat aspects of the hypothetical skill. So it seems like a tricky design problem. That would be less of an issue for officer skill picks - if you have a dedicated carrier officer, that's fine - but since those come from the same skill pool...
Overall, I'm happier with the skill system now that it doesn't have these (well, almost - Point Defense, still) and the carrier effects are fleetwides-only.
I think you're really overestimating things here.
Only the small minority of min-maxers would agonize over wasted bonuses. The non-carrier players (or at least those who don't personally pilot them) would simply ignore them either because it is irrelevant to their play-style or found that trying to squeeze fighters into non-carrier ships for the sake of utilizing those bonuses more trouble than it was worth.
Meanwhile, giving carrier/fighter exclusive bonuses to existing skills would help the Carriers get out of their current bad standing.
Besides, what options do you have? You have said that Carrier exclusive skills are not an option, and yet at the same time you consider adding carrier/fighter bonuses to existing skills as some kind of design sin that will ruin everything.
So besides leaving them in the rut, that leaves either designing a whole separate (sub)-system for the Carriers/Fighters (And if the debacle behind the Colony system is any indication, this is not your preference)... or removing them all together to prevent obviously inferior newbie trap options.