It's also due to PNJ that Naruto got caught by chakra rods in the first place.1) Nagato wanted to capture Naruto - he had to hold back.
2) He brought Naruto down with his chakra rods - Hinata had to save him (well, she had to die ^^). Naruto would've been dead long ago if Nagato wanted to kill him.
3) Nagato had already fought the whole village = massive chakra usage.
4) Because of plot no jutsu Naruto wasn't attacked by all paths at once.
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Naruto was ready to take out Deva path right then and there, but then this happened.
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So let me get this strait.... Instead of dodging and attacking Deva Path, he catches Pa preventing his use of shadow clones or reverse summons to counter Deva Path. That was actually plot heavy for Pain. It was also plot that Naruto didn't turn into the 9 tails at the start of the fight.