Based on what I've seen here, people are saying that Naruto would beat Pain based on the fact that he not only resisted but also redirected the force of a Shinra Tensei back on the latter, but he also forced Pain to move closer to his main body and because Pain was cautious of the Nine-Tail's power; he created an extra large Chibaku Tensei which exhausted him and caused him to start bleeding profusely. Looking back on the chapter, Naruto did put up a good effort against Pain, but the thing is I can't ignore what EndDancer said. Pain was already sort of exhausted from all those fights and the massive village-destroying Shinra Tensei beforehand, and now on top of that he had to fight Naruto in his Six-Tailed state, who was stronger than expected and required a Chibaku Tensei to rein him in.
My other reason for placing V2 Naruto below Pain is because a near full power Pain was able to create a crater this large with Shinra Tensei:
This was the power of Naruto's Tailed Beast bomb compared to that:

The crater a nearly full-power Pain was able to create dwarfed the size of Naruto's Tailed Beast Bomb. As we all know, after Pain used the village-destroying Shinra Tensei it drained his chakra by a lot, which affected his performance against Sage Naruto and the toads, and he continued to use smaller scale versions of it against them too, the biggest one pushing the toads out of the village. You could argue that it is implied V2 Naruto can beat Pain because Pain praised a weaker version of Naruto, Sage Mode Naruto, for being the toughest opponent he ever fought, but remember, he praised Kakashi as well, and he defeated him relatively easily. Well, he did lose his second strongest Path in the process, but compared to the Deva Path, Pain doesn't focus as much chakra into the others as he does into the latter. I feel like had Pain been at full power, he might have either not have needed to make a insanely large Chibaku Tensei to seal Naruto or he might have not needed to make one at all; a large Shinra Tensei similar to the one he used to take out the village may have been enough to beat Naruto.