I find myself making a new save for each spaceship I create. This is simply because the distances in the game are rather large and the beacons disappear when you are too far away. (I have an idea to remedy this as well, but more on that on another thread.) What we need is a tagging system. Essentially a beacon that is tied to the object's field of influence and moves along with it. In other words, mobile beacons.
The cool thing would be being able to save these tagged objects separately into a new save. You could tag an asteroid, save that asteroid into a new save, and load it in another save. Of course this comes with a few problems like the loading. You could simply load the asteroid into the new save in it's original coordinates but there's a chance it would load inside another object. In my opinion when loading a tag the users should see a ghost image of the object and be able to place it themselves wherever they want.