Before Naruto entered the fight:
- Pain defeated the whole Konoha including Kakashi, the same can kinda be said about Tsunade, and don't forget all the really strong Jounins (InoShikaChou father trio and other Konoha 11 relatives (those who have them, AND that INCLUDES Hyuga clan), Hokage ANBU squads, Ibiki, Shizune, Ebisou, ...)
- Pain used the big ass Shinra Tensei and had an enormous handicap since he couldn't use it at first when Naruto entered the Battle (if he could it would be so over for Naruto)
+ he was trying to capture Naruto
And still Pain with all those handicaps would still win if the Kyubi wouldn't have interfeared or if he wanted to kill him he could have before the Kyubi would ever even get a chance to interfere
+ The 6 Paths of Pain are ONLY one technique Rinnegan has to offer, after They would have been beat (which they wouldnt) Nagato still has 7 or 8 (depends on weather you count the YinYang chakra seperately from the Ying chakra and Yang chakra) elements, + a shit load of techs, strong Fuinjutsu and ofc the Gedo Mazo
+ after the enormous chakra consuming Chibaku Tensei Nagato had enough stamina to revive the whole Konoha