Why Nagato wins...
1: We are talking about Nagato, not the 6 paths of pain, meaning that he has all their powers in one and if we go from edo form, lets say hes young/healthy prime so on...
2: I admit that Naruto is super fast now and stuff, but that doesn't mean nagato can keep him in check, force pull will do the trick

and also he can use the summoning path to increase hes field vision sight.
3: Any ninjutsu on nagato wont work.
4: Even with BM, Naruto is fast but he cant teleport or use space time like tobi/minato, that means he will get pulled by the gravitation of Chibaku tensei, we dont know its range yet but I asume its pretty long though.
5: If he captures naruto with bansho tenin, he can use the human path technique in order to seal hes soul or whatever he does... dead end and naraka path for capturing him then king of hell inside the statue would kill him..
6: Bijuu Dama, 2 examples, first, he can blew naruto off while he charges bijuu dama with shinra tensei or let hes summons disturb him, second, he can block it because bijuu dama is made of pure chakra IMO. Toad summonings works for naruto but one shinra tensei on them and they are dead.
7: He can absorb narutos BM chakra and if he does that he will even become more powerful lol and naruto would just stand there and like ... Kurama ??...
8: Km bunshins, Shinra tensei them bansho tenin them or capture them with naraka path abillity,
9: If Nagato uses human path abillity on Naruto then hes dead. (said it twice sorry) xD
10: Asura path abillity missiles will keep naruto busy and he needs to use rasengans to destroy them. You cant destroy missles with mere hands.... thats lol .
11: Sage mode, we saw how sage mode worked vs 6 paths when they had wasted like all of their chakras after destroying hole konoha lol
what more can u say?