I'm giving thumbs up to the Krell four-parter.
SPOILERS TO FOLLOW!!!!
The resolution of why Krell was acting that way was a surprise for me. At first I was a little disappointed. I had considered it, since Krell was sent in to replace Anakin, while delivering orders sending Anakin directly to Palpatine, but it was down on my list of possibilities. Ahead were things like being prejudiced against the clones, having had a bad experience with the clones, being a dunderhead, knowing something we don't. My initial disappointment was because those possibilities, which I had thought were played up, might be reduced to red herrings. But then I realized I felt disappointment emotionally because I was disappointed that as a Jedi of admirable warrior qualities had fallen. In a way [i.e. from a certain point of view

], all those possibilities higher up on my list are really true and not just red herrings. In particular, he was prejudiced against the clones because he thought they couldn't win anyway.
From my experience, this is certainly a high-water mark for grittiness in a cartoon aimed at children. Given our recent and still ongoing wars IRL, this is probably not a bad thing.
With respect to the issue of the clones exceeding their conditioning, it's inevitable that it will come up. Now what's really interesting is that this four-parter has, as others have pointed out, provided a fascinating justifiable context for Order 66 not stated in ROTS:
to kill Jedi because they are collaborating with the enemy. And here we have a fallen Jedi who was doing just that. ROTS provides no text of Order 66, and the current EU text of the order, given at
http://starwars.wikia.com/wiki/Order_66, states an unsurprisingly broad context for the order:
In the event of Jedi officers acting against the interests of the Republic
This shows that TCW is measurably improving upon the text of the PT, by adding depth to that which was rendered on screen only vaguely and with broad strokes. When word gets out about Krell, clones should believe Jedi can turn traitor, and their execution of Order 66 will not necessarily just happen in accordance with blind faith. Oh, what was missing in the PT!