DC Universe Online did a very good job at this,
any item had a connected visual (of a certain set) that you collected on equip,
you then could choose in a tailor like screen what visuals you actually want to see, the stats of the item stayed the same of course.
In STO (and Champions) it is strange... sometimes the visuals are bound to a certain item, or they are freely available in the tailor screen (well C-Store stuff not so freely, but thats not the point here).
Anyway i have read multiple times now that dStahl wants the KIT's (and possibly Armors?) to be included in the Tailor instead of bound to the item.
I guess that would be a first step to give us customizable kits (instead of the sub-optimal pre-defined 4 packs).
I don't think that the way ship visuals work, or that Weapons visuals will change anytime soon.