I think it would be a neat idea if, for every ship you purchase in the C-Store, you also get a holo emitter of that ship's image that can be equipped on other ships.
Let's say you purchased the NX-class replica Light Escort in the Enterprise bundle, for instance. It's a cool ship, we heart it. But it's only got 3 weapon slots and is therefore only really fun for a vanity ship or for a new character.
But if we also got a holo emitter device, like those purchasable with gold-pressed latinum, that projected an image of the NX-class, we could also then enjoy our purchase every once in a while on our higher tier ships.