Can't believe I never posted this one. I still find this hilarious.
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Naruto started the fight already with 5 free frog summons + slug feeding him intel from every previous fight pain was involved, so he didn't need to figure out which body had which ability + aiming to destroy with Rasenshuriken + prep time Senjutsu filled Kage Bunshin to extend Sage mode
Pain couldn't aim to kill + spent resources already fighting in Konoha, one of the fights being Kakashi + used a bunch of chakra to destroy Konoha + Deva Realm was nerfed from the start.
And Naruto still needed Hinata intervention and 8 tails.
Naruto was rushed into battle whilst he was still supposed to be training so he was hardly fresh either, nor did he have much time to formulate a plan with the information Katsuyu provided. Of course it helped, but he made his moves on the fly.
Shinobi of Pain's calibre don't come at their opponent without the intent to kill. They just exercise enough restraint to avoid actually doing it. Even Naruto and Sakura came at Kakashi with that intent during their second bell test.
Pain was hardly low on chakra considering he didn't run out until the revived all those that had fallen. In the end lost because Naruto timed his attacked.
There's really no telling how that fight would've ended if Hinata hadn't showed up. I think Naruto could've broken free one way or another.