I do agree that being able to sell or trade ships would be a neat idea but I would much rather prefer new units. Actually, what I'd really like are more buildings.
You know that space between the planet and the area you can build in? Wouldn't it be awesome if we could build orbital platforms or a ring around the planet (think Conquest: The Frontier Wars). Habitat rings or platforms to raise population caps. Extra hangers for fighters and builder ships. Defense platforms with flak guns and other weapons to help defend the planet (especially from siege ships). Research platforms to increase research speed. Stuff like that.
It'd be also nice to build deep space platforms (other than the super defense stations). Something in the areas without colonizeable planets and asteroids. You know, a Deep Space Nine sort of deal or Babylon 5. Whether for just defense or to add an extra population and resource center. It could also allow you to build in that area.
And more upgrades for planets would be nice. Besides emergency services to increase planet hit points and reduce damage taken from orbital bombardments, there should be a slot for silos and other terrestrial defenses. Surely missile silos exist. Is it not feasible that they could fire missiles from the planet at attacking ships? And more research centers planetside.
I was kind of hoping for troop transports. Although I guess colony frigates and the capital ship count as this, but additional uses would be neat. Such as boarding actions to take over ships or to decrease the time it takes to capture a planet.