Naruto does defeat pain with the help of kyubi, just after Hinata shows up and he is incapacitated, don't you remember?
From the wiki:As they talk, Pain is attacked by
Hinata Hyūga, who makes a desperate attempt to save Naruto. The Deva Path deals with her easily and apparently kills her. Her seeming death enrages Naruto, causing him to enter a
version 2 state. Unprepared to fight Naruto in this state, the Deva Path leads Naruto closer to Nagato's location so that it can use
Chibaku Tensei. Naruto enters a nearly full
Tailed Beast Mode and escapes its confines, forcing Pain to let the Chibaku Tensei dissolve.
I kinda agree on the second point, but it does remove a lot of stakes and is a big fake out at the same time, which are some of the main criticism of wano. (Not the only ones)