The fight with Nagato was NOT as one-sided as you think. Nagato had just done away with Jiraiya.
Jiraiya:
1. Rasengan
2. Sage Mode
3. Shadow Clones
4. Shima and Fukasaku
5. Swamp of the Underworld.
Naruto:
1. Rasengan
2. Sage Mode
3. Shadow Clones
4. Shima and Fukasaku
5. Kyuubi
Now keep in mind that the Kyuubi only helped Naruto out AFTER all the other paths had been beaten.
Jiraiya managed to kill four bodies, animal path dying twice.
MEANING that Nagato had just fought a Sage Mode user that uses more or less the same techniques as Naruto. Also, Akatsuki has certain amounts of intel on their targets...
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How the hell did Tobi KNOW that Naruto ended EXACTLY two lives in one attack without being there?
Let's pull up the experience defense because I know somebody will...
Did experience keep Deva Path from falling to a Rasengan?
"Pain wasn't trying to kill Naruto".
Well guess what, Naruto can't kill Pain either. Bodies are dead. Meaning that in order for Naruto to truly beat Pain, he would have to conserve energy and hold back so he could take down Nagato himself. OR, Nagato would just find new bodies and attack Konoha again. Naruto wouldn't have truly taken over the threat.
At the time, was Pain stronger than Naruto? Hell yes. But it wasn't a total assbeat like everyone thinks..