Nothing so broken as other suggestions.
Idea's pretty simple really: You "capture" disabled enemy ships during combat by hovering close by, in the same fashion as a capture point. The conditions you have to meet are that the wreck is intact, and you have enough marines on the ship(s) doing the capturing - So a combat frigate with a crew of 30 probably won't be able to take control of an Onslaught.
Another possible pre-requisite is the ship(s) carrying those Marines also have a boarding pods hullmod or weapon - and all Marines are split across those ships - Lose one and you lose a lot of Marines.
A short while after successfully capturing a wreck, it will be flown off-map in a similar fashion to a mothballed ship. This will guarantee its recoverability and reduce the supply cost (Handwave: The Marines put out the fires. Handwave 2: Those fires are what kills the remaining crew in the absence of Marines) to do so. It can still be re-destroyed while attempting to exit the map, at which point it's 100% guaranteed to fragment and be irrecoverable, along with most of the Marines in it.
The intent is to create more dynamic, emergent objectives within battles, while also allowing the player to be more selective with which ships they attempt to recover, and give certain ships a purpose within combat. You could have a non-combat personnel transport ship for the sole purpose of recovering prised enemy ships - it gives your enemy a target, and you something to protect. Or, you can down-size your crews to have room for Marines on most, allowing you to use swarms of boarding-capable ships to both capture and protect a wreck, at the expense of CR.
Where it gets icky, as usual, is how the game would work out how many marines vs crew are on what ships, or if the player would have to do that manually (Something I think we want to avoid; I wouldn't mind, but I'm not the entire playerbase).
There's also the issue of accidentally capturing wrecks you don't want, just by Marine ships being close enough for long enough - maybe this could be avoided by having to give an order specifically to capture a ship before the process can begin (except for player ship?).
Finally, there's also the fact that wrecks will maintain their inertia and eventually drift off-map. Maybe a tractor-beam type weapon, or some kind of equipment that can be used to halt drifting wrecks?