Nagato fought konoha, destroyed it, fought Naruto, used Chibaku Tensei and revived the dead in Konoha. His stamina was great. His physical condition didn't restrict his Chakra level. After absorbing Hachibis Chakra, his body just got regenerated, it was like a power thrust from a foreign source. It is also known that Naruto is regenerating his body with a bit of Kuramas Chakra. And I think that it's clear that Nagato is not going to put out his Chou Shinra Tensei at the very beginning of the fight, he will keep a good fight techniques which will may exhaust him and put out his strongest Shinra Tensei if needed. Yeah, Nagato fought the whole Konoha but actually fought fodders, except of Kakashi. Asura Path crushed a few buildings, such as the summons, Ningendou pulled out two, three souls, and so on.
Just take a look at
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. Those elongated rocks in the surroundings are huge and comparable with houses of Konoha. Now take a look at
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picture. On the left part of the first panel you can see a large area with those rocks which are spreading across the whole area but look actually small, though being comparable with houses. So we can actually compare this area with a village; means Konohas size isn't considerably larger. And yet we see Susanoo destroying a meteorite first, before causing a shock wave which is devastating a distance with the size of the area I showed you and is even continuing to travel
after it cut several mountains. I'm talking about a single swing of a sword Susanoo was holding in just one hand, not considerable how terribly the Kages would have been crushed when Susanoo was about to swing its sword by holding it with both hands. A single swing of Susanoos sword is indeed comparable with Nagatos strongest attack. Or do you think that Nagatos strongest Shinra Tensei would be able to crush Madaras huge meteorite in pieces,devastate a distance comparable with a village and destroy a distant mountain range after? I highly doubt it, even if Nagato would be healthy.