I've decided to only use federation sanctioned weapons throughout the game (photons, phasers, quantums.)
But, there are fine lines on some weapons. For instance, tetryon, although its not a sanctioned federation weapon, it was still used by dax in DS9. There are other examples, too, jsut curious what you hardcore trekkies thought about some of the weapons and their "fine line" in federation canon.
From a ship perspective, I think it is more important that players figure out what type(s) they want to primarily use, and to specialize their skills accordingly. You can do heaps of damage to enemies like this.
On the ground, use whatever you like, and keep in mind special properties that help in certain situations (like enemies with strong shield regen powers).
Overall, I'm a serious Trek fan, but I think game play and "fun" factor need to be the top priorities in a game.