I'd have to re-watch bad batch, because I can't remember if directly said. But you'd think a part of the empire is afraid of how easy it was for them to have the Clones turn on the Republic and Jedi, and fear that someone could do that to them.
Obviously the droid armies had reliability issues, and were probably exposed to the same weakness of programable betrayal.
Brainwash some humans, that's gonna take time to undo, can't just turn a whole army against their current leadership all at once.
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