You could combine a bone system with just flat cards, yes, but that would propably be a first. It also depends on how you want to create the animations. With fixed animations you would model your assets just as usual in a 3D app like Blender and then export them to egg Actor files and animations. Then bones are only needed in that 3D app. If you want to create the animations on the fly based on physics then you have to worry about bones in Panda. Don’t know how those are done … via connection points like in the Looking-and-Gripping sample?
Alternatively you could create a 3D game and then use the cartoon shader and a fixed camera position to produce a 2d-like effect. You propably already saw this topic: [Pixel-art Sprite Cards)