I watched The Last Battle again and realized something when Rex was talking about his programing and how it was broken in a very few Clone Troopers. I think it was a nod to the Season 2 Clone Wars episode The Deserter. In that episode Rex is wounded by a Commando Droid sniper team and is left with a family whos father is a Clone that deserted the GAR after the First Battle of Geonosis. It's one of my favorite episodes of the series and puts a different light on the Clones.
That, and the early arc of the 6th season which released online