[dmm]

To me, it seems that real world fighters have 4 advantages over ships:
1) Much faster. This should be easy to implement in a mod.
2) Much harder to hit, due to: a) small size, b) speed, and c) maneuverability. This should also be easy to implement in a mod.
3) Separate units, so you have to kill them one at a time. IRL, big guns are useless agains fighters, not just because they can't track the fighters, but also because this tactic is incredibly wasteful of supplies. This could also be implemented in a mod. Ideally, the hard code would be changed to prevent any weapon from killing more than one fighter at a time. But one could simulate the effect by giving fighters and missiles a very high defensive bonus and giving PDC a partly offsetting offensive bonus. The net effect would be that regular weapons would still kill a whole lot of fighters in a group if they hit, but they would almost always miss, thus canceling out the mass-kills on the average. (So if your dreadnought had lots of shields+generators or organic armor plus it had a quantum converter, then maybe you could plan on using regular weapons as fighter defense, but otherwise this would be a sure-fire losing tactic.) A simpler solution is just to not let regular weapons target fighters at all, ever. IRL, if you have an all-battleship fleet with no APC and get attacked by a carrier group, you're dead, end of story.
4) They can get close and choose the exact target area for their weapons. In SEIV, there are no "critical hit" rules, so this translates as much higher damage for a given vehicle size. This is readily modded.

On the other hand, IRL fighters have these disadvantages:
1) Much more limited supply. This has two effects: a) They have to be transported to a battle by a carrier (or refueled enroute, with advanced tech), and b) Long battles require re-supply by the carrier, which takes time. In SEIV, we have a difficulty, because we want fighters to have a high speed (e.g., 10 just for starters so they have a battle speed of 5) but we don't want fighters zooming around systems. Part of the solution is to give them small supplies and make their weapons use small supplies. Thus, they can zoom around during a 30-turn battle but can't go more than a few sectors before running out of supplies. The other part of the solution is to make fighter weapons of three kinds:
Large size, large damage, large reload time, and medium tech weapons that can only target ships (i.e., torpedoes, anti-ship missiles);
Small size, medium damage, large reload time, high-tech weapons that can only target fighters (i.e., air-to-air missiles); and
Small size, small damage, firing every turn, small supply use, low-tech weapons (i.e., machine guns).
2) Much more fragile. Fighters should be hard to hit but easy to destroy. (Same with missiles BTW. Drones too?) Since SEIV insists on grouping fighters, you'd have to reduce the damage done by PDC also. The reason for doing this is to allow fighters to destroy each other in dogfights with their "machine guns" but not allow "machine guns" to take out a heavily armored/shielded dreadnought.
3) Their carriers are fragile, not very fast, single-use vessels. They don't have the internal structure to carry heavy guns. If you can mod in a rule that carrier hulls can only carry regular-size weapons, then that would make things more real and also help with the exploit mentioned by someone.

That's all I can think of for now. Hope this helps.