A mix between the 2 technics seams a good choice. The hardest in 3D is to make realistic human characters and to animate them properly, that is why they go for the very design look for the 3D Clone Wars series.
I guess I could say: landscapes and interiors in 3D and photoshop matte painting, and characters in 2D (exept some creatures that can be made in 3D then transform with a 2D treatment).