To combat the Borg cubes and over-fitted drones, every component in a drone should have a 3rd cost: deployment cost. In a match, every time you spawn (including when login in a match) this deloyment cost would be tallied. At the end of the match, it would affect negatively your total score (something like Total Score/(Deployment Cost*Times Spawned) could work). That way, players are encouraged to get better so they can keep up their performance while building the most bare-bones drone they can.
This has even been speculated to be the 3rd, yellow numbers in the DRONE editor, but it's hjasn't been confirmed.