Personally I think a complete revamp of how the weapon model functions in the game is needed.
1) Differentiate ships more with new weapon types (e.g. Beam lance, beam turret)
2) Add new firing arcs (at least port and starboard)
3) Differentiate weapons more by optimal and maximum firing range
4) Make some weapon slots on ships require a set type. So all Federation ships would generally have at least one beam array for example.
It would be nice if ships were only firing one or two individual beams at a time, to reduce the visual clutter. If we had a weapon model more similar to the Star Fleet Command games' we'd have a lot more space for new ship types to expand into.