Yes but that doesn't take away these advantages of such a system:

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2) If I decide to tweak some common scene like attack or walk cycle, I would not need to edit every single model for this.

3) Model files could be smaller (?)

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I think this would be a really great improvement.

It could be implemented like this:
The bone animations are saved to an external file. This file contains the bone names and their rotations/translations for every frame.
For every model, a skeleton with the same bone names as in the animation file is created or imported and then the vertices are attached.
You then use ent_animate to animate an entity with the given scene from the given animation file. Bones that don't exist in the skeleton are ignored.

A similar system is used by 3ds max (Biped system) and it works very well.