Board Thread:Versus Debates/@comment-9782468-20150219204421/@comment-1018594-20150219221425

The Nine-Tails Chakra was the biggest deciding factor: Pain had Naruto beat until he transformed into his Version 2 form.

Assuming he knows nothing about the Rinnegan and the Six Paths of Pain, Minato's speed is his only advantage. Pain was able to withstand senjutsu and absorb Rasengans, both of which were Minato's other skills. Minato can summmon toads, but as we saw, Pain's summons were able to occupy them. I'm not even gonna mention nature transformations because Pain has all of them.

The unexpected element of Minato's Flying Raijin is greatly compromised by Pain's shared vision. The Deva Path can use its gravitational abilities to mess with Minato's kunai, so his usual teleportation might not work as effectively. More than likely, Nagato will know that Minato plans to mark the Deva Path and will sacrifice the other Pains to protect it, knowing that they can be restored.

Minato just doesn't have the firepower to take out all the Paths in succession. His usual one-shot kills won't be very efficient due to the Naraka Path's restoration, and Pain will drag the fight out until he eventually wins.