i`ve has a bit of an idea, just recently and well its a pretty good one. Ok, so say you have desructable universe and battleship encounters on your mod.. Would it be possible to add to their loadouts a token or medal so that if you kill a nomad battleship you get a "Nomad Battleship killer" token. This would take the form of say a shield gen which offers no other advantage. The tokens themselves could be added on top of themselves (like ammo) so that when your ship is scanned you have a history of the major enemies that you have beaten.
You could also add, "Pirate Base killer" or "millitary/police base killer".. The only prob though is can you mount new equipment internally? And, if you can (don`t think so), how could you re-transfer it when changing ships? It would need to be mounted on to hard points which would limit the amount of token slots available but what`cha think? Worth a go?