Clone Wars Season 6.
I have to say, Season 5 was actually really good, there were at least two arcs during it which were really rather good.
The arc involving Death Watch and Darth Maul (and his brother) was, by a long way, a favourite of mine. Darth Maul actually succeeded in being one of the most interesting characters and it was awesome watching him fight Obi-Wan again. The other arc involving the framing of Ahsoka was actually also pretty good, and possibly the first time I actually came to appreciate her as a character.
On the other hand, it looks like the series ended with a lot of the stories unfinished. Particularly, judging by the entries on Wookiepedia, it does not finish the story of any one of Darth Maul, Asajj Ventress or Ahsoka Tano (none of whom appear in Season 6, which I did spoil for myself by reading the ends of their Wookiepedia articles). Ventress seems to be present in some of the other Star Wars Legacy (Extended Universe) content, but even then it looks like the content never covers her death... Plus it actually looks like some of these extended sources conflict with some of the Clone Wars stuff, so it's not particularly great.
Darth Maul's story on the other hand appears to end with his last appearance in Clone Wars (I.e. being tortured but not killed by Darth Sidious) and similarly following Ahsoka leaving the Jedi Order there is no mention on whether she is hunted down following the execution of Order 66.
Overall, the three major character's whose fates are NOT determined by the films are left completely open, which is something of a travesty.