This is a problem that has plagued game developers for years: this aspect of 'balancing' everything so the game runs smoothly (if you've ever played any Call of Duty multiplayer, I think you'll agree balancing the game is tricky).
The problem here is, standardising the weapons would cerntainly help to improve the game (ATM, the Sovereign seems to overpower all other ships), it still leaves the problem of the individual hardpoints. Deadthunder has already mentioned the issue with the Akira; the only way past that would be to give it low-damage torpedoes or remove the excess launchers. In my experience so far, when I've asked people to beta test mods, is that a ship can be balanced against some ships - but completely over/under-powered against others. I've always tried to slot my ships in with Kobayashi Maru, and use it's standards where possible.
This idea is excellent, but it will require much thought and testing in order to reach some kind of balance. I do hope you'll attempt this project, because a standardised set of weapons would be a welcome addition to the game.