Shinr is spot on, that's definitely part of my thinking. It also makes balancing battlecarriers more tricky, but that's more of an issue with dedicated fighter skills. Putting their bonuses on elite skills is an interesting idea, though, hmm.
The main balance problem with fighters is that they can snowball very hard. In theory, having capable anti-fighter AoE damage would mitigate this (you have more fighters? that's great, the effective DPS of the anti-fighter AoE just went up because it's hitting more targets) but for it to work with the actual game mechanics, the area of effect would need to be larger than what looks reasonable, and the weapons would need to be very common. Of the vanilla weapons, I think only the Devastator and the PCL fit the bill; possibly also the Paladin PD, to some extent.
And so, fleets that don't have *a lot* of these get snowballed by fighters, and minor bonuses to fighters stack up extremely quickly. A fighter being just a little tougher to destroy or doing a little more damage adds up to enemy ships being overwhelmed in a non-linear way.
So - this is why the main buffs available to fighters are fleetwide skills that are capped in their total bonus. It helps rein in this scaling, and it seems very difficult to accomplish that by giving flat fighter bonuses from officer skills - you'd likely end up with a scenario where you can stack enough of these bonuses and get past the tipping point.
And as far as the general gameplay, I think a state where fighters are a little too weak is much, much preferable compared to the state where they can snowball like this. That *is* subjective to some degree, but I feel strongly that the gameplay with fighter-spam fleets is not particularly interesting, beyond the novelty factor.
I could definitely see buffing fighters a bit, though - just, in similar ways to how it is now, with fleet-capped bonuses that are more resistant to snowballing effects. And, IMO, this largely rules out skill bonuses - although, for example, the "use a hullmod to give bonuses based on skills" idea could be used to get around that, if the calculation also involved the number of fighter bays in the fleet, somehow. Or heck, if the skill effect did. But that is also getting quite complicated; I wouldn't want to hang that onto every skill.