So I was looking at the crafting systems of other games etc when a though came to mind.
IF an extra component/material was used, why not let us craft non standard items?
Example: Undine rep, Bio resonance focusing lenses (or some other named item) is needed to craft a Bio beam weapon of X type, not just the beam banks but also twin beams or even Omni.
I think adding some kind of a system like that would help to increase the diversity of the weapon loadouts, not just for reputation based weapons but even Retro phasers etc.
This could also be done with ground based weapons too.
Example: Borg shield modulation scanner would allow you to create anti borg weapons of different types (pistol, rifle etc) and of different energy types.
This is a rough idea and would need to be worked out more, but generally speaking, I think this would be good.