I enjoyed both series, but I feel like it's apples and oranges comparing the two.
Clone Wars was awesome and focused on short bursts of action, setpieces, and neat motifs, basically quick glimpses into the Clone Wars; while The Clone Wars was also awesome, but focused more on "feature-length", character-driven story arcs and progression.
If I had to pick, I'd go with The Clone Wars, simply because it was more engaging and had more depth.