In regards to the faction specific class-9 weapons idea, I would just like to say that it's a great idea... but then I've always used the guns that suit me best, regardless of their faction of origin. I feel that's part of the game, that you can customise your ship to suit your fighting style however you'd like. It's not a massive stretch of the imagination to say you've salvaged guns from downed hostiles, in SP that's practically the best way to proceed and succeed.
That said, I hate equip-to-win. I see the most unbalancing weapons in the game as the Tizona and Colada class weapons, as one fighter can effectively neutralise the shields of even the biggest ships. Without them, fighters struggle (as they should) and capships have the strength they were intended. Gunboat Infernos are fine against fighters and gunboats alike, there is absolutely no need to mount Tizona class guns on one. I plain don't like 'em but I guess that's just my gripe :0P
With current weapons it is fairly easy to destroy even the heaviest of fighters in about 3 seconds flat using an equip-to-win attitude and half decent aim in an opposing heavy fighter. Perhaps hull damage specific weapons for fighters could use a little gentle downgrading?