The only way to do the "2x dmg vs fighters 0.9 vs traders" thing is if you changed their stats versus specific shield types and then restricted each ship to a shield type.. Not gunna happen. :)
As for the gunboat. I agree that the gunboat should be tweaked a bit.. but moreso the weaponry. Now Igiss has enabled a way to restrict guns to certain ship classes. The gunboat turrets should be increased in damage slightly to make them alitle better. Though nothing too extreme like that damn Order Mk2 turrets wtih 4k/2k dmg.
EDIT:
Ooh! Another idea.. increaese the accuracy of the gunboat anti fighter turrets!!! :D that would be a excellent fix.