I don't know if I'm reading too much into this, but in a recent interview with executive producer Daniel Stahl had this to say:
In a recent interview with Subspace Radio, you mentioned that you are considering ways of being able to craft ships, specifically within fleets. Can you elaborate on this possibility?
One of the additions you can build for your Fleet Starbase is a Shipyard. As the Shipyard progresses, it will unlock the ability to make new ship variants. Whether or not it is directly tied to the crafting system is TBD, but the notion that you build a Shipyard to gain the ability to make these new ships is valid.
Is he implying that we will be able to use the shipyard in our fleet bases to unlock and build new types of starships?
The fact that the word "variants" was used probably means only visuals... still, nice.
Especially on the KDF side, there's usually little opportunity to mix-match a good-looking ship.
Edit: I've got a Very Rare Phaser Relay Mk XII and I can't sell it due to the EC cap, if anyone is willing to trade it for a Very Rare Mag Regulator Mk XII, contact me.