Again...?
1) Naruto had a hard time fighting Nagato EVEN after Nagato fought him AFTER DESTROYING A VILLAGE.
2) It was not a 1v1. Nagato alone, with his Six Paths of Pain, fought against many other opponents, which include Kakashi, Chouji and his father, etc. And not to mention, the rest of the ninjas he fought to find out naruto's location.
3) Naruto had had help from the toads... or frogs? (Gamabunta etc.)
4) Konoha had intel Nagato and the Akatsuki, while Nagato had no knowledge of Naruto's abilities.
5) Even Konohamaru played a part.
It just means that the whole village was against Nagato. However, Naruto was the only one who could make use of the advantage he had and, barely, won Nagato. In fact, all he did was to defeat the Six Paths of Pain, NOT Nagato. So, IMO, Naruto + SM was never enough to become stronger than nagato.