[@Akayaofthemoon][@Pathfinder]

Compounding on this conversation (if it's not rude of me to join in)
[Hider=Free Will]
I believe the Gems are given their free will in order to work more efficiently. Sure, a mindless drone would have consistent results across the board, but that would be their greatest weakness: consistency. 

When one is stagnant in the heat of battle, using the same moves and tactics every single time, the enemy could start to read their movements, predict them because it is almost guaranteed that they would use them, and diminish the drone's possibility of success immensely as the battle continues.

A gem with free will might not be able to succeed in their task as much as a drone, but they are more flexible, capable of thinking for themselves, to get past the blockage in their path through multiple means instead of the only path in a program. A free thinking gem could be unpredictable, fight with desperation and concoct tactics that no "efficient drone" could ever dream of executing for the sake of their goals.
[/Hider]

That's my thought on the issue, anyway. Take it as you will *shrug*