Well, Anakin/Obi-Wan/Anakin's apprentice (aka Short Round v2) are annoying. I haven't been able to stomach most of it, but there was a good story (I think it was two episodes) involving the clone troopers with none of the big characters where they had to stop a Jedi who was literally trying to kill a bunch of clones by tricking them into shooting each other. That was good. I'd watch a show with the clones were they pretend Anakin either doesn't exist or that he atleast isn't the biggest whiner to ever be a jedi. However, they don't do that, and so much of Lucas's stupidity just ruins the show in general.
My favorite Star wars book series (which is probably also in my top 3 book series of all time) is the Star Wars Republic Commando books. Lucas single handedly made them pretty much outright lies by turning Mandalorains into hippes just so Boba can be a loner and the last violent Mando. That alone makes me hate Lucas more than Episodes 1-3 combined. I personally pretend he didn't do that and Mandalorians stayed a warrior culture, but the fact remains is that he screwed up my favorite books because he's a hack. The hilarious thing is they can't even really be taken out of continuity (not that I want them to be, but I'm talking from the perspective of people trying to make the show fit the EU/vice-versa), because some of the characters in Republic Commando played a small but visible role in the Legacy of the Force books, so its just a big clusterf%$k at this point. He also went against the sensible "Twilecks and Humans can't have kids" idea and created mutant abominations that really make no sense. How does a human have a kid with an alien that literally has part of its brain hanging from tendrils in its head? Thats really pushing the human/near human Star Wars stuff. I can accept a human and many different species, but the Twilek/human hybrids make about as much sense as Human/Wookie would make, just because of the Twileks most obvious biological feature being incompatabile with humans. This isn't a huge deal, just another example of idiotic writing.
Overall, The CLone Wars is just an outlet for more horrible writing on TV to mess with the Star Wars Universe. Its something I can only stomach when it has absolutely none of the big characters in it, but since thats not generally a focus, the show just sucks.