Since it came up in a recent battle...
We're trying a house rule on Anti-Fighter Batteries: they roll to hit, needing 6+ to do one point of damage, before the attacking fighters roll to hit. The number of dice you get is equal to your undamaged hull. Any fighters that are destroyed do not get to make the attack.
The reasoning is that bigger hulls will have more "AA" guns, especially since they allocate more space for AFB than smaller hulled-ships. It was a last minute idea, so we haven't had a chance to try it out; but then most of our ship designs don't have AFB because they are not cost-effective.
(some time to think passes :? )
Hmm, this doesn't work when you move and attack with one flight at a time. We had been moving all the flights and making one big attack. An option to the above house rule could be that the target ship could choose to fire just some of his AA guns and save some in reserve. The target ship has "hull" amount of anti-fighter weapons to shoot at attacking fighters per fighter phase (they could also be used to shoot at attacking drones).
Another idea came to me: bigger hull ships increase the chance of a fighter being destroyed based on the fighter attack roll. So instead of just a 1, a fighter takes a hit on a roll of 2, or even a 3 on very large ships. I looked at a commonly used chart (i.e., the explosion size chart) but that is too excessive. Perhaps this might do? Hull size/roll that destroys a fighter: 1-8/1, 9-24/2, 25+/3.
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Btw, does an attacking heavy fighter that rolls a 1 becomes destroyed or just takes 1 point of damage if the target ship has operational AFB?