The day Nagato easily deflects 5 TBB and does it in an instant at the same time, and manages to knock the TBB around, and knock 5 bijju without even using a jutsu...is the day that I say Nagato is up to par with Naruto. Until then...Nagato has NO way of defeating Naruto.
Shinra Tensei: Naruto in 6tails mode has already been shown to be able to reverse it..Bijuu mode could do it soo easily.
Chakra Absorbtion: Naruto has already countered that by feeding him sage chakra, hand to hand. Naruto will easily beat pain, not only cuz of his sage mode, but his new found speed, which intails a bright flash, speed, And power.
Bansho Tenin: Nagato pulls naruto in...and then what?..LOL. Naruto can just dig some chakra claws into the ground to stop himself from being pulled in, or use them to attack nagato. Also, he'll be pulling Naruto in..what happens when he gets a hold of naruto?
Soul taking: he tried that on Naruto, and it was the same process as the Kurama/Naruto tug of war. It COuld work maybe...but the fox will just tell Naruto to kick nagato in the face..Naruto himself wouldnt think of doing that.
Chibaku Tensei: Naruto can just make a TBB and blow that shi up. Or, just simply "flash" to nagato and attack him.
Summons: If Naruto Bijuu mode is solo 5 other Bijju....Nagato's summons will mean crap
Chakra Rods: Naruto has already been shown to resist the control, and to overpower it with the fox chakra
Gedo Mazo: With up to seven tails who knows..Both Gedo mazo and Bijuu mode have been shown to wreck havoc. I think we are about to see that fight very soon, Naruto Bijuu mode VS Gedo Mazo. I think in that case it will go either way.
This may be biased...But for good reason. I mean honestly, what can Nagato himself do?