First off, I'd like to say that I was going to place this on the "6.x" thread but I wasn't really sure that that would be the right place. If it was then please move it away. Anyway, the suggestion:
What I was thinking about was having an option on the New Game Menu to restrict or limit the weaponry choices to either Missiles or Beam/Kinetic Weapons for both the NPRs, Spoilers (Perhaps with the exception of the Invaders) and the Player.
It could be like this:
Missiles only game: Missiles, Drones, etc..., as the only offensive weapons. Beam/Kinetic ONLY as PD (Can't target ships or they have really poor accuracy).
Beam/Kinetic only game: Beam/Kinetic as the only usable weapons. Missiles would only be able to be placed on Mines. Drones usable but only on non-combat (Geo/Grav Survey) or semi-combat roles (Active/Thermal/EM Sensors).
I believe this would be a great option for the game, allowing currently semi-useless or very situational weapons like Plasma Carronades or HPWs to be effective.