Fighters changed quite a bit with time, both lore-wise and in their implementation. At first the carriers where supposed to have a mini autofactory onboard and the fighters were merely an Universal Access Chip with some limited uses you plugged in, thus the limited replacement and the obligation to have a flight deck to support your fighters. Then the fighters became ships of their own, only needing a carrier to be repaired in combat as long as you had replacement chassis available, but otherwise not bound to a flight deck if any. And recently with CR everything got muddier, they got some form of invincibility, being impossible to wipe out as long as a carrier remains, and kinda immune to harry since even at 1%CR they can deploy at full strength. They also can be part of a fleet regardless of the availability of a carrier, with often the lore-breaking sight of a fighter-only fleet casually cruising in hyper despite not supposed to have any hyperdrive...
What I'd like to see, if the fighter effectively becoming the
weapon of a carrier. Intuitively it makes sense as carriers are force projectors: they are useless without fighters, and fighters don't have the range (or the hyperdrive) to be useful without a carrier.
In term of gameworld, the fighter would become and UAC again that allow the carrier to build them on the fly in combat at the cost of it's own CR. The carriers would then be cheap to deploy (routhly the cost of a combat ship of the same power minus the flight decks), but rebuilding more fighters would raise that cost, and of course rebuilding a Talon wouldn't put much of a dent in it's CR while a broadsword wing would lower it a few percents. The fighters would be traded not like ships but like weapons and be installed on the carrier during refit like as usual, with each flight deck able to maintain two wings (one wing per deck seemed a bit low):

In combat they would still behave as they currently do: you can give them orders, and deploy them or not (but only if their carrier is deployed too, otherwise they would never die again). The carrier would probably have some sort of limitation to avoid eating all it's CR in one battle.
One suggestion from Gothars was to have the rebuilding take more and more time once its CR drop bellow 30%.
What issues would that solve:
- No more carrier-less fighter fleets. If the carrier goes down, the fighters too. If the wing survived the pilots can be rescued, but the fighters can't be maintained or rearmed without the corresponding UAC.
- No more exploit of super heavy fighter fleets that only have one carrier just to prevent their death.
- No more obscure cost of fighter deployment due to the losses. The carrier CR recovery is all that matter.
- Better control on the amount or fighter replacements. If you want more Piranhas, you only need to deploy that wing and not any other: the carrier will spend all it's CR to rebuild that one.
- Lootable fighter wings. As any weapon, an UAC could be found in the post battle looting.
- Clean Lore explanation that support the gameplay instead of excusing it.
[EDIT]
Tentative mockup of what it could look like in campaign:

I replaced the "1 flight deck" with an icon of the installed fighters, and linked them to their carrier in the widget.