I feel the balancing between different player counts (specifically going from solo to 2-players) can be made more even if, rather than Buddy being an all-or-nothing addition, he could be assigned his tasks (i.e. split the tasks that he performs like refilling ammo, gunner, on-foot support, etc into a a checklist of individual tasks)
The amount of tasks you can enable at once could then scale depending on how many players are on the ship via some sort of input device or UI element (maybe in the initial area of the mission?).
For example, if there were 10 tasks, have the amount you can enable could be 0, 3, 5 and 10 for 1,2,3 and 4 players respectively.
Lore-wise it could be explained as his power runs off the same system as life support, so the more life that needs supported, the less he can do.