nagato is not stronger than naruto would give him a good fight but not better this is my reasoning for why naruto>nagato:
naruto has most of the counters on nagato
Naruto has shown that even his six tailed form can not only resist shinra tensei but push pain back and i know you are going to say he wasnt at full power but neither was naruto not even close to it.
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nagato using regular shinra tensei on naruto would be to his disadvantage as he would be pushed back
and naruto in bm can deflect tbbs which destroys mountains way more powerful than nagato's regular shinra tensei
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he even beat bansho tenin with his chakra arms with ease
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And mind you nagato has limited mobility while naruto is incredibly fast i dont have to post links for that. And naruto has a counter to preta path which is frog katas or plain shuriken used as a knife like how minato threatened bee during their meeting
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And we all know that naruto can use sm clones alongside bm/km clones hell they kuruma can even protect his clones etc when nagato attacks with asura or shinra tensei like he did here for gai and kakashi
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asura path is almost useless against the like of naruto and in general not too effective.
naruto has his own summons that can occupy nagato's summons rendering his shared vision to be less useful add in a km clone there to help out the toads and nagato's shared vision would be effectively lowered.
Human path is not too useful when naruto has multiple clones out who can help him and you have to consider the fact that naruto is also generally too fast for him to be caught in it. And if he does he isnt in a disadvantage like when he was during their last encounter since he has clones that can save him instead of itachi, and we all kno the clones where elsewhere in the battlefield and that was not even close to naruto's full potential.
And we know that CT is useless on naruto now as he is has tbbs to save his ass which which naruto has been able to spam. naruto has a counter to everything nagato has to offer. And lets add naruto's advantage he is faster, has clones to make a hell of a lot more distractions and has a LOT MORE CHAKRA ofc including kuruma and sm which can natural energy on its own. l
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Naruto wins the fight with mid-hard diffuculty especially consdiering the fact that nagato has low mobility and if a clone and bunch of toads can occupy his summons making his shared vision a lot less effective making him a lot more vulnerable as kabuto mentions here
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Naruto beats Nagato its silly how far ppl push nagato he is one of the best in the show but current naruto with his full arsenal beats nagato.