The lack of balance (And mass whinage that follows the lack of balance) have actually pushed me away from the Discovery mod for the most part. I'm now playing "Freelancer: Combat Evolved" which has been released. It's probrably one of the most hard-core communities I've seen. Balance is achieved by only letting ships use specific weapons. (hard coded into the mod)
You get a Missile Frigate, your using missiles, no questions asked. It's a sigh of relief honestly as noone gripes about balance. You can either fly your factions class of ship well, or you just plain suck. Theres no "You have better weapons." or "Your ship class is unbalanced with those (insert other ship class weapon name here)"
All in all, what I'm trying to say is perfect balance is not possible without the quality of a funded development. Even then it becomes harder with the more items you put into the game.
Honestly, myself I have been waiting ever since I started Freelancer for a modification that has standardized loadouts for every ship. IE, you get what comes on the ship, nothing more, nothing less. With FL:CE I have that. As for Discovery ever getting something like that.. Highly doubt it, but I would *love* to see it happen.