Although I highly doubt this will ever be used, I would like to propose an idea in regards specifically to the appearance mods given to ships by some equipment.
After thinking about the possibility of player armor and kit visuals to be turned into costume options, I thought why not do the same thing with starship appearance mods? It would solve several issues in one strike, as well. To sum it up; some players prefer the look of one part or set but the stats of others, and starship appearance mods do not carry over during Saucer Separation and Multi Vector Assault Mode.
If acquiring a part that adds an appearance mod to a starship were to unlock the appearance mod in the starship editor, not only would players who are both appearance and stat conscious not have to worry any more, but it could even allow for ships like the T5 Galaxy Refit and the Multi Vector Assault Escort to display the appearance mods on all sections of the ship even while separated. It could even allow pre-existing set parts to have additional "costume pieces" without actually adding any new pieces of equipment to the sets in question, e.g. the Borg appearance parts from the assimilated carrier in "The Cure" and Donatra's assimilated Scimitar from "Khitomer Accord".
Like I said, I highly doubt that the awesome people at Cryptic would approve of such a proposal, but I and hopefully many others would love it if this idea were to be used.