So we all know that Pain apparently controls people through the use of piercing made of a reactive material that reasoned to high frequency chakra waves. And seeing how Jiriaya and now kakashi reacted to pain chakra emitted through his eyes, I wanna say that the Rinnengan actually disrupts and redistributes chakra and he uses the redistributed chakra to emit a form of control over all those who have piercing in, what probably is, chakra points on there bodies.
The only real evidence I have is (MangaShare didnt Have it up at the time)
It disrupted chakra flows, probably redistributed(Maybe) and it allow Pain to summon more bodies, because Sage Chakra is more powerful then regular chakra, and the weapon that he used on him that cause his chakra control is probably made of the same material as the Piercings which lead to, what i believe, redistributed his chakra only to make him stronger.
Thoughts..... hate mail..... tell me 5 other threads have this same theory....