I liked the art style and action of the older Clone Wars series, not least of all because my favorite Jedi held her own against Grievous and his MagnaGuards in it.
However, the newer series is unbelievably good, very serious, thoughtful, and mature if you give it a chance. It's done a wondrous job of fixing Anakin's character whiplash between AotC and RotS.
And it's actually a step above the rest of things as canon goes, since Lucas is personally involved in production, beyond his general yea/nay role in most of the EU. For instance, one storyline included a Mandalorian dueling Obi-Wan with a cortosis vibrosword. Lucas shut that down immediately because nothing solid is supposed to be able to block a lightsaber. So it was changed to a new ancient Sith "darksaber" and added a bit of interesting mythos to the whole thing.
And really, Anakin and Dooku dueling through the series is no big deal. Their lines in RotS don't need to be referring to AotC, as both are rather prone to pre-duel posturing.