phyomin

The owner of Rinnegan created all ninjutsu, taijutsu and genjutsu.
How could he be? He may have the power that can sense both spiritual energy and physical energy.
How could he sense these energies? He may have huge amount of the spiritual and physical energies and could also be aware of it. The manga has also prove that Pain has very big amount of chakara. Later he could use these chakara to manipulate elements (wind, fire, water, earth) at his will and whatever kind of jutsu.

What is the difference in the Sage Mode of Naruto?
Sage of Atmosphere and Earth is not the kind of technique that uses the user's chakara bit by bit. The owner of this technique draw incredible amount of chakara from the surrourndings around him/her (such as atmosphere, earth), combine it with his/her spiritual and physical energies and create the new kind and infinite form of energy. It is just another, very much higher and advanced level of technique.
In the real world, it could represent new and advanced renewable(never ending) energies which could b very useful and not harm the world.
while rinnegan may represent old form of energy using. very powerful yet but have many disadvantages and harm the surroundings.
Kishi may be the green lover
Naruto is using sage techniques which could surpass ordinary jutsu(s) including six paths (highly modified but in the same way in using just two spiritual and physical energies lack of natural energies). He may lose at first because he need to understand the flawless and great of his new technique and to be enlighten in Sage of Atmosphere and Earth. The green energies also have limitations now and just imagine beyond when the limits are broken down by someone
You remember? Naruto is the first and only one yet in his kind. He will surpass all before him

In conclusion, Rokudou Sennin was the fonder of old era and Naruto will b the fonder of new era. Naruto is the gifted one with the power of toads.
See here: http://www.onemanga.com/Naruto/376/15/

It is just my opinion and let me know ur opinions too.

Viczor6

Intressting. green lover :P

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sarutobisensei

green lover
nice theory