It might be an 'issue' with ISA fighters specifically, if it's really an issue. I know ISA is meant to have the best fighter squads.
The ISA Heavy Fighter Wings (the ones with 3 ships, 2 Auto Blasters each, and shields) completely wreck other fighter squads, and I've watched a single fighter wing kill frigates without taking any losses. Even if they did take losses they'd be replenished by a carrier, whereas the frigate they killed is just dead.
Plus, fighters have the advantage of being effectively immune to friendly fire and collisions. They never get in the way, like frigates do.
That said, maybe frigates are just early game ships. Once you can field a carrier, fighters are the way to go and it's working as intended, i don't know.
The ISA Heavy Fighter wings don't appear in the Simulator so I can't test them against a variety of frigates in a more controlled environment.
As for frigates, the Order-Class frigate is absolutely a beast with a good setup. It's a really fun ship, but they can die when the AI flies them, unlike fighter squads with carrier support.
After flying the Order for a bit, my beloved Kentucky-Class Cruiser seems so sluggish.