The Clone Wars is a terrible show with strokes of brilliance.
As much as a continuity disaster introducing Ahsoka was, I really enjoyed seeing what unfolded with her in this final arc. You really get to see how the Jedi Order and the Republic are falling apart and all the seeds of mistrust have been planted. For a character that was introduced to cater to young children, those that grew up with her must have an odd sense of dread about what has become of her now. Gripping stuff to be sure.
The biggest fatal flaw in the arc though is what they did with Barris Offee. I know she only had maybe a total of one minute of screentime from the films (and that's pushing it), but she did have a character arc outside of that as well. I'm usually the last one to say "you can't do that, it would contradict the expanded universe", but I remember the official site had an exclusive story to subscribers about her prior to the events of Order 66, and I think the TCW team knowingly dismissed this. Normally that's not a big deal, but it seems like the whole reason they used Barris instead of some new Jedi was her connection with Ahsoka, which seemed to have no baring whatsoever on Ahsoka's choice when it was all said and done. So essentially it was all for nothing. Also, this is a character that was the goody two-shoes of the universe, and hasn't been on the show in about three years. Now we see her for five minutes and she is a murderer, a mastermind, and a terrorist for the "greater good" of seeing the Republic fall.
Still, every once in a while, this show amazes me, and this is one of those times. The Krell arc from last season was probably the best the show has done, it's just unfortunate that for every good arc, there are at least 6 terrible ones. Also, bringing Darth Maul back from the dead was a terrible, terrible, terrible idea.