From a very good Wired.com interview with Star Wars: The Clone Wars Supervising Director Dave Filoni..
Wired.com: Given all that’s happened, where does the series go next?More Clone action is always welcome as some of the Clone-centric episodes have been the best of the series. Including one of my personal favorites, "Deserter."
Filoni: It’s exciting. We have a lot of it figured out, but I’m always personally projecting the end of the war. Especially dealing with the major characters, like Ahsoka and Rex.
But I will say that the second half of this season, which I think really began with the “Nightsisters” episode (view clip above), is where we really get into the large arcs of the show. We start marching in a much more chronological order than before, where we were jumping around from character to character.We’re going to have a major clone arc coming up, as we develop Rex’s character, and the same goes for Ahsoka.