Ok sure its possible Pein's puppet master isn't Nagato but lets assume he is for now.
I was thinking Pein is pretty effin tough. Each Realm has some pretty crazy powers and the 6 together as of now seems almost unbeatable(some may disagree but whatever). So I got to thinking, if they find Nagato is he gonna be some pushover who's hiding behind the 6 Realms? Or will he be Naruto & Co worst Nightmare?
See thing is Nagato killed a Chunin as a child with no training. We don't know how but the guy was pretty F'ed up...
After 3 years he became a pretty accomplished ninja...
So lately I've really been thinking the true master of the Rinnegan might be much more of a problem than his pawns. And he must be pretty strong to get use of so many strong bodies against there will or if they joined of their free will. And after everything the only thing we know for sure the Rinnegan can do is PWN a Chunin in a brutal way.
Oh and a side note. I'm pretty sure Konan being a pupil of J-Man and comrade of Nagato and Yahiko, is far from as weak as everyone thinks. Just cause Jiraiya made her look stupid doesn't mean anyone else can.