I wonder if any Clone Troopers resisted Order 66? (Spoilers)
In Episode 1 of Season 6 (available only on Netflix) Clone Trooper Tup has a meltdown and kills a Jedi and can't think of why he did it.
His Sub-conscious genetic programming glitched and Order 66 kicked in ahead of time.
If that could happen then could other Clone Troopers who, unlike Battle-droids, are not rigidly fixed to their programming, resist Order 66 and spare their Jedi commanders?
That would explain why a few Jedi survived other than Yoda and Obi-Wan.
I could imagine some episode of 'Rebels' where a remorseful Commander Cody is featured leading rebellious Clone Troopers against the Empire.