Well, it definitely has some advantages. If you use it in the way I described above you'd stick with regular animations until something happened to the model then you'd switch control to Natural Motion. The extreme advantage this would give you is a ragdoll whose limbs collide with his surroundings realistically. With regular animation even if you are detecting collisions your model's specific limbs can't react to anything, all you can do is perhaps reverse an animation (that's what I do in Geisha House).
So, if a box rolls down a hill and you detect that it collides with your guy you surrender him to NM. His legs would get knocked out from under him and he'd try to catch himself. His goal would be to get right again, and when he did you'd simply switch it back to normal animation.
Right now if that character gets hit with the same box and you turn him into a ragdoll he'd get tossed around like he was dead. To right him you'd have to let him fall then morph him into a lying position then animate him standing up. The effect is okay, but lame compared to what NM can do. NM controlled ragdolls are actually trying to survive and correct their balance.
All that being said, it's still not a good way to perform normal animation. Imagine this - you're animating a normal model, and it's invisible. You have a ragdoll right on top of it. The limbs are tied to the animated model's limbs. Every time the animation moves it pulls on the ragdoll limb and attempts to move it. The difference is the limbs will stop if they touch something - a rock, a wall, a sword, etc. That's not exactly what NM is doing but the effect is similar - your guy would flop around like a rubber zombie. It's a fantastic new way to do ragdolls but at this point that's all it is.
I would absolutely love to combine Advanced Animations with NM. Imagine - perfectly blended animations combined with intelligent ragdolls.
Come see the WIP!