We went for "Only One" pilot in a fleet of a thousand ships.
Then we added "OnlyOne" Enemy.
The ships that have no pilot can only do very basic actions like fire blindly, drop EMP or flee. the piloted ship can order those actions to nearby ships.
The enemy is a planet like ships that you have to "dig" to reach the core and kill.
The game is called OneOnOnes : https://itch.io/jam/gmtk-2019/rate/463229