We know he redeem his death to recover konoha people which at first give his the pain of losing family and best friend. His death is a sacrifice. Nagato's position as the leader of Akatsuki was well-deserved, being its strongest member and, as Pain, being called unbeatable at different points by Konan, Fukasaku, Tobi and Zetsu. Jiraiya was frightened by news that Pain killed Hanzō by himself, as not even the combined Sannin in their young age could defeat Hanzō.
Kabuto Yakushi also regarded Nagato with hindered mobility as his second strongest reincarnated shinobi, behind only Madara Uchiha. Indeed, it took the combined efforts of Itachi Uchiha also a reincarnated Akatsuki member, Killer B and Naruto a perfect jinchūriki to seal Nagato. But yes as in manga Naruto the one who defeat him and become hero but let be serious uzumaki > all.
We know he redeem his death to recover konoha people which at first give his the pain of losing family and best friend. His death is a sacrifice. Nagato's position as the leader of Akatsuki was well-deserved, being its strongest member and, as Pain, being called unbeatable at different points by Konan, Fukasaku, Tobi and Zetsu. Jiraiya was frightened by news that Pain killed Hanzō by himself, as not even the combined Sannin in their young age could defeat Hanzō.
Kabuto Yakushi also regarded Nagato with hindered mobility as his second strongest reincarnated shinobi, behind only Madara Uchiha. Indeed, it took the combined efforts of Itachi Uchiha also a reincarnated Akatsuki member, Killer B and Naruto a perfect jinchūriki to seal Nagato.
Yes, Nagato was indeed a very powerful shinobi. Being the leader of the Akatsuki, he was just about stronger than anyone, and literally unbeatable... But don't forget that he was able to accomplish all that because of the Rinnegan, which you're probably aware, belonged to Madara.
Just so you understand it better, let me give you a little insight of Naruto vs Pain fight:
1. Nagato was using the Six Paths of Pain. This means that his chakra was being distributed evenly among every Path, so every Path received 1/6 of Nagato's chakra, which means that Nagato could only use 1/6 of the total power of his jutsus from each Path using the Six Paths of Pain.
2. On top of that, Nagato was channeling his chakra to the Six Paths of Pain, so the strength and speed of his jutsus was considerably decreased.
3. On top of using 1/6 of total power which is further weakened by decreased strength and speed of jutsus, Nagato had already used so much chakra in his battle against Konoha. He fought so many shinobis including Kakashi, not to mention the almighty Shinra Tensei which destroyed the entire village. All of this activity prior to his fight with Naruto consumed a huge amount of chakra, so he started his fight with considerably depleted chakra levels.
4. On top of using 1/6 of total power which is further weakened by decreased strength and speed of jutsus, and having used so much chakra before and slight exhaustion, and even on top of losing all the other Paths including the regeneration Path as the fight continued, he easily fought Naruto and effortlessly pinned him down using only the Deva Path.
5. Even after all the aforementioned reasons, and fighting with only the Deva Path, he could have easily killed SM Naruto, only if he wanted to. Since Naruto was a jinchuuriki, he couldn't kill Naruto. So, Naruto had a tremendous advantage due to this restriction.
Therefore, the conclusion until now:
Deva Path only (with an immensely depleted chakra reserves and considerably exhausted, and the strength and speed of his jutsus decreased, and even having no intention of killing Naruto) > SM Naruto
6. So now we have a severely weakened, exhausted and low on chakra reserves Pain (Deva Path only, mind you) who can't use the maximum strength and speed of his jutsus, and has no intention of killing Naruto, even after that he was able to counter Naruto's six tailed form, full of rage, and fought on par with him.
7. EVEN AFTER ALL THOSE DISADVANTAGES ON PAIN'S SIDE AND Naruto's sudden burst of power thanks to Kurama, Pain was able to dominate Naruto using Chibaku Tensei.
So now, let's take a look at Naruto's state:
Deva Path ONLY (weakened, exhausted and low on chakra, decreased strength and speed of jutsus, plus no intention of killing Naruto) > SM Naruto + Six Tailed form (enraged)
8. Even after ALL THAT, Naruto was completely owned by Pain. So he had to push further and unleash the eight tailed form, only then he was able to fight back Pain with the upper hand.
Let's summarize again now:
SM Naruto + EIGHT Tailed form (enraged) > Deva Path ONLY (weakened, exhausted and low on chakra, decreased strength and speed of jutsus, plus no intention of killing Naruto)
OK, so that's what it takes for Naruto to overpower Pain. Impressive!
8. Even after all that, Naruto completely ran out of Sage Mode while Nagato still had enough chakra to revive so many of Konoha's shinobis. Even then if Nagato wished to destroy Naruto, he could have easily done that, unless Kurama intervened again to save Naruto.
Nagato said it best who his main opponent was:
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BTW, we've already seen how well Nagato could handle Naruto, Bee and Itachi combined, during the war. If it weren't for Itachi's Totsuka Blade sealing and saving Naruto and Bee on time, they would've been in serious trouble.
Sorry, but the reality is... Uchiha > all. Uzumakis are really powerful, but every other shinobi/clan pales in comparison to the Uchihas.
Nagato Uzumaki was only so powerful because of Madara Uchiha's Rinnegan, and Naruto Uzumaki is no match for Sasuke Uchiha without Kurama.
Uzumakis are only good for making themselves strong by attaining external powers, because their capable and potent bodies as well as immense chakra, stamina and vitality make them probably the only clan who can innately handle external powers. Uzumakis own their own are no match for the Uchihas.
