A really cool plot twist could be that Naruto actually befriends one of Pain's bodies during the fight. Through their interaction, he manages to turn that body against the others. This would add a whole new dimension to the fight and the story, as it shows Naruto's ability to find common ground even with his enemies and use it to his advantage in defeating Pain.
Another plot twist might be that Pain has a hidden motive for attacking Konoha that is completely different from what was originally thought. And Naruto, in the process of defeating him, uncovers this truth. For example, Pain could be under the control of a more powerful enemy who wants to test Konoha's defenses through Pain's attack, and Naruto has to deal with this new revelation as well as defeat Pain.