I don't think that the current flexibility of joint hierarchy is really needed. Even the modification and reconfiguration of joint hierarchy is a seldom used feature I think. I couldn't think of a situation where non-joint "real inner" nodes are needed. The only thing that could be needed is to attach a node to a joint, like in the knight example.
AFAIK the current collada converter writes model data only, so real scene resources could be only created with hand or a custom editor.
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A scene (level/map/world) definition is something that is quite application specific and usually includes more than graphics data (entities, gameplay data), so it does not make much sense to have a "sample implementation" in the engine core.
I agree with this, too. While I quite like your editor, we chose to create a game entity centric level editor.