I view the key problem with Fighters being that SD didn't quite decide whether they were a ship, or a weapon system. They opted for a bit of a hybrid approach.
Fighters auto replace (great, but that is like a weapon)
Fighters auto upgrade (Nothing else in the game does this, and Fighters benefit from MANY upgrades because they use components, like a ship)
Fighters are super mass effective because they get capacity upgrades in time and auto upgrade, and are a ship with no engine, gaining them more space.
Fighters are hard to deal with because they are a single target and have to be hit by the same type of weapons mean't for much larger ships, and ships can only target one ship. Leading to a quagmire battle when fleets run into them and have to hang around murdering the fighters.
Personally, I really would have preferred Carriers/Fighters be treated more like a unique weapon type, than a ship in a ship. This way, unique anti-fighter equipment could be brought in to balance them, that would target them specifically, freeing major weapons to work against enemy ships. Thus, a carrier only fleet would get chewed up by a regular fleet, as it has no escorts, the attacking fleet will certainly take a bruising from the fighters, but they won't SLOW DOWN to deal with them, they'll head straight for the carriers and murder the threat from the source.
Treating fighters as a piece of equipment (fully) also means they won't auto-upgrade, and won't benefit from capacity tech either. Furthermore, Fighter's attack could be a very low attack of all three weapon types, making them useful generalists, but not capable of fully compromising an enemy fleet that just doesn't have the right defense.
Right now, they are ships in ships, but with none of the downsides of other ships and very little cost.
Finally, I wouldn't mind letting fighters conduct bombing runs on planets, allowing you to specifically kill certain buildings or something like that