I'm not the biggest fan of the new series in general, but the main reason I don't like Ahsoka is the gaping hole she leaves in the reasoning of the characters and events in Episode III and afterwards. Since she doesn't appear in the events after the show, it's only logical to think that she either dies or disappears/leaves. In either of those cases, don't you think a character would find it worth bringing up at some point during Episode III? Especially in a scene like the appointing of Anakin to the council and when he eventually betrayed the Jedi?
In the actual show I feel like they could have presented her in a better way as well. Her character is basically a smaller (and more annoying) Anakin, and I think she is part of the reason that characters like Asajj Ventress are underestimated when she can stand up to them in a fight while being just a padawan. I understand that the writers probably wanted a character for the show's teen viewers to relate to and like because of her "rebellious" attitude, but to create a character that important in Anakin's life doesn't make sense when she is never mentioned in any of the events afterwards.
That's just my opinion, so take it with a grain of salt.