IGN had the chance to interview Dave Filoni, and in the interview Dave revealed what the final arc of Star Wars: The Clone Wars would have been about. It sounds like it would have been a very compelling and interesting arc if it would have been released:

“That was somewhat of a challenge, but I kind of just put it to my mind as if I was writing this and we had never made Clone Wars. And I was thinking,
It is the last story arc of the Clone Wars TV series that we were doing, was this story about Ahsoka and how she crosses with Maul. What was significant about that was that it was the story that was really going to draw her possibly back into the Jedi Order, because the motivation around this conflict with Maul was her knowing the personal history between Maul and Obi Wan, who was their dear friend. So she was caught up in that, and basically she says point, “The last time I saw Anakin, he was rushing off to save the Chancellor.” She was actually planning with Obi Wan and Anakin the capture and attack that would get them Maul, because she had figured out where he was towards the end of the Clone War. But before they can go through with this plan together, Obi Wan and at one Anakin get called away to Coruscant to save the Chancellor, which leaves her with Rex – and some other exciting characters – to basically go and deal with Darth Maul, once and for all. That’s kind of a good brief of what that was about.”

If you’re as big of a The Clone Wars as I am than you know how amazing this arc would have been. Never give up hope that we won’t see this in some type of medium. While I would love to see this on screen it’s more likely to come out as a comic book or a novel. Hopefully we get to know soon!