I'd like to be able to capture a defeated ship, without giving up my existing one. A way to do that might be to require having a relevant Officer on staff (Pilot or one of the space-combat specialists, for example). That worthy then flies your ship to either the nearest planet (which may not like you), or (preferably) to a specified planet, and places it in Dry Dock. You have to go there to pick up your officer again, and to access the newly-captured (probably damaged) spaceship.
(This post is duplicated in the Officers thread, 'cause it seems to be related.)
Another neat extension would be the ability to take over an Alien ship. For this you would need one of the Anti-Alien Officers to commandeer the vessel, and some sort of "conversion" Upgrade at the space Dock before you can use it yourself.
That might (eventually) lead to being able to get non-standard equipment (alien ship comes with a "death ray" that does missile damage, but does not use up missiles, for example).
...and all this leads to the concept of scavenging or cannibalizing prize-ships.
There should be a way to refit features from one ship into another. I would say it has to go in the same Upgrade Slot (which must be available), and you can only get one such feature from a prize ship, which will destroy the ship (unless it is a replaceable Upgrade?). Perhaps you need to be at a "major" star-port, where you have sufficient rank/reputation to get this work done. Or, maybe the Mechanic or some other Officer(s) need to supervise this kind of conversion.
Just having this mechanism in play would also address one of my minor pet peeves - I should be able to take my combat-suit/ground-vehicle/etc. with me to my new ship, if that Slot is available in it.