Star Wars Kanan 4 and 5 - finishing out the arc, the story had finally gotten interesting in #3 and stayed interesting is 4, but unfortunately had to compress the actual interesting part to get us to the end of the arc, which was based on some pretty dodgy character work that will resonate throughout the canon (all new Marvel comics are in-canon) for clones, namely that Order 66 was a momentary thing, not an ongoing one. This leads to a moment that finishes the tale which borders on deus ex machina, and also requires a visual narration that the character we're in the memory of can't know. I dunno how to call this.
Sounds pretty sloppy. Who is writing this?
The pattern I am noticing is that Marvel/Disney is putting a-list talent on the "Star Wars" series. But, that talent may well be working under too many mandates to do their jobs well. "Darth Vader" had a scene that read like "somebody wanted Vader to visit with Jabba in the first issue dammit", which was far beneath Gillen. The impossible flashback you mention may have been similar. ("We need to show this, here, even if it does not make any good sense.")
-edit: Just read your review at SSG.
That's a pretty deep shift, it asks a lot of the audience to accept that the clones are still "good guys" who only had a momentary, forced lapse in judgement, yet still serve blindly without that programming's influence. Do they serve the Galactic Senate or only the Chancellor? Do they have qualms about the blatantly wrong acts they're ordered to do? If they served on the Death Star and were deceived into serving, does that not invalidate the moral victory that Luke and the Rebel Alliance enjoys in the destruction of that facility? A lot of potential ramifications come out of that change.
I am not sure it is as deep a shift as you are saying.
I assumed that Order 66 was a contingent order, planning for the sort of thing that nobody likes to think/talk about but those in power need to consider.
Consider "Case Red" (a US plan to invade Canada that was considered viable until WWII). Similarly, the Feds and military do have plans to put the US under martial law if things break down too much. (Soldiers will be stationed away from the areas they are native to, to maintain loyalty to the Feds, not local institutions.) These are not tin-foil hat stories. They are "worst case scenario" plans.
I always figured that Order 66 was some kind of contingency against a coup or other mischief from the Jedi. (It would be a terrible enough prospect that the Republic would have been lax not to account for the possibility.) If we assume that the Chancellor is the Senate (as he identifies himself in Episode III), then serving one is serving the other. And, following orders would be a result of training/conditioning more than brain-washing.
"Innocent parties on the Death Star" has been a question among fans for decades.