There is make caps more realistic against fighter-bombers without totally ruining it for the lighter ships.
Take flak and make it an almost zero damage weapon but give it this effect: it throws the ship around violently that it hits (smaller ones only hopefully can be done).
A big advantage smaller ships have when attacking a larger one is to fight back the larger ship has to fly in a straight line in order to fire turrets.
This gives fighters--which are already a hard target--a real advantage in hit ratio. Flak would even it out.