Hmmhmm... the ships could have more than the primary and secondary weapon of the first Wazzal. After all, these are large military conflicts . What about something like this : there are three weapon sizes, small, medium and large. These can be either fixed or mounted on turrets. For example, a small fighter or shuttle might have small, fixed cannons. Your modded transport would begin with one fixed mining laser - a medium weapon. Corvettes, assault transports, gunships might have small turrets and a medium fixed big gun. Battlecruisers would have medium turrets and one or two heavy big guns. And the Evil Alien Battlecruiser would have lots of heavy turrets and a death star-style superlaser .
Add some nifty gadgets - a cloaking device, a turbo booster, drone fighters, EMPs, ECMs - and you have a very nice combat system .
You could customize your ships' arsenal freely, but getting really powerful military-grade weapons might be tricky and if one of the factions doesn't like you it might use possession of illegal armament as an excuse to shoot you down on sight.
You could have a very neat reputation system, with the factions reacting to it. If you haven't actually attacked a Quasi-Quintupletian ship, for example, they couldn't blow you out of the sky without a good excuse - it would be a PR disaster. But if you do things like looting QQian ships or associating with the evil, fachist dictatorship (according to the QQians) of the opposing faction, they could try to make your life very uncomfortable with a variety of other ways - collecting huge special tolls whenever you visit their colonies, sending assassins disguised as pirates after you, seeing to it that you become collateral damage in an unfortunate accident.
Of course, allying yourself with the Evil Alien Marauder would end up uniting the rest of the human race against you .