The Season 6 Lost Missions have some really great story arcs that set out to explain plot-holes in Revenge of the Sith – the first being the whole “Order 66” Jedi-kill thing, and the other being the weird moment at the end where Yoda is like “I have discovered how to appear as a blue ghost” to Obi-Wan, which seemed weird and forced.
The latter storyline is mainly notable for the bit where Yoda goes into the scary cave in Dagobah and is confronted by evil, angry Yoda.
The Order-66 storyline is also good, because while it feels a little stretched it also sort of makes sense of things that don’t ring true with the chip theory – for instance, like how was a damn chip not discovered in all these clones working right under the Jedi.
In a widely shared tweetstorm re: the Prequel Trilogy, Glendon Mellow expressed some doubt re: the Order 66 chip theory. He says that he preferred the (now non-canon) version of events where the clones did what they did out of a sense of betrayal. However, I’m not sure that’s right on a viewing of Revenge of the Sith.
All Palpatine says to them is “Initiate Order 66” – which suggests that they knew exactly what Order 66 before the order was given. Even if they did know about Order 66 beforehand and the Jedi never cottoned on, its a logical leap to suggest they heard the Order, which to them meant the Jedi must have betrayed the Republic, which then gives them the motive they need to overcome their affection for Jedi in order to murder them.
In the Clone Wars we frequently see clones question their orders and react in typically human ways to things. The “betrayal” theory goes along with this – they feel betrayed, therefore Jedi must die – but they have no personal knowledge of the betrayal at all, so on an emotional level it doesn’t work.
And finally, if it was a conscious decision, in at least some instances (not least, Commander Cody’s), you’d expect some hesitation – even if it was only momentary. Instead, they just pull out their guns and start firing.