The missiles aren't a problem, can easily mod them... it's what the rest of the interface allows. The devs really should consider this in the upcoming expansion pack.

As for overall balance, yeah I'm still working on the integrated patch (fleet / mothership / missile mods). Kept putting it off because I thought there'd be updates to this mod, heh. You're pretty much spot-on about the weapons; I'd also been actually considering removing the higher-tier turrets and expanding light gun types. My experience was that at high levels the mothership pilot Bryna&KT turn your ship from a carrier-type into a battleship-type. I often tank battles with it solo without even launching my fighters, that's just wrong lol. Besides, I find 4 tiers of each weapon excessively redundant - how many players even bother with the tier 1 or 2 guns anyway?

Problem is the game only technically recognises 2 types of damage, laser and other. Plus shields are a universal type anyway, aside from the additional laser defence modules - which only few ships carry. There's barely any difference between lasers and particle accelerators (both laser type), and plasma is also similar damage/rate-of-fire except that it isn't laser damage. We can play around with rate of fire, damage, dispersion, range... that's about it I think.

Edit:
Combination mod finished. It's around 30+mb minus the voice pack (I think I'll let you guys download that separately, it's 50mb). Where should I upload this?