Originally Posted by Uchiha Barles
A couple of things: we don't know that the third's clones are on a higher level than Naruto's. That's a third interpretation that holds no more or less water than the two I mentioned. It might be one of those skills that is the same for anyone who casts it. If the third were to cast a million clones like naruto does, each might be just as weak. We simply don't have enough details about the workings of the technique to know what interpretation is correct, if any, which is why I ventured more than one.
Another thing is, taijutsu does take chakra. From what I've seen, after losing chakra past a certain point, even your taijutsu gets weaker. I could simply just be misunterstanding the link between chakra and stamina though. I'll admit that I'm not following that. Furthermore, the gate openings are taijutsu techniques, and those clearly require at least a flow of chakra. It stands to reason that if less chakra is flowing, that technique might be less effective. Something similar might apply to kage bunshins.
The last thing is, how do you know the chakra is returned at all, upon dispell or upon destruction of a clone? I haven't seen that in the anime, and I started reading the manga around the chasing sasuke arc, and haven't seen that in the manga either. This is conjecture, though I suppose it is an educated guess with good basis.
Ok, I forgot to address one thing in your post, the stamina thing. Kakashi did also mention that there was a stamina requirement to keep a clone active, which is stamina that he himself did not possess to make that training useful to him. So basically, to make this technique work, you need the following:
1) Create clones that have enough chakra to be useful for training.
2) Have the stamina to keep them out long enough for the training.
Anyone who can do these things can use this technique. You're right. But, who do we KNOW can do this besides Naruto? Specially in regards to the second requirement. Also, who do we KNOW can do this better than Naruto as regards to both requirements?