Pain was forced to shinra tensei the multi shadow clones ganging towards him. Pain was unable to execute jutsus for 5 seconds and Naruto is rushing towards him with a rasengan at hand. So that makes perfect sense.
No it doesn't ****ing make perfect sense. When you can withstand getting crushed by massive boulders head first and block off hundreds of chakra blasts (each stronger than a rasengan), you can survive a simple rasengan at point blank.
Yeah he had theoretically 5 seconds delay between each jutsu, but go tell me there always were 5 seconds everytime he used it. He always used it whenever he felt like it, the "5 seconds" crap only came into play when Naruto had to use plot-no-jutsu to win.
Whoever said Goku only used Kamehameha should go watch the anime because he only fires that skill a few times, and it doesn't really end the fight.
Seriously you guys disagreeing with this are just being Naruto fanboys, you know very well what's being discussed here. Gaara only uses sand but he has a lot of sand jutsus. Gai, Lee, A, Tsunade and such use hand to hand combat but have many ways of going about it. Naruto really only creates a diversion with a kagebunshin and then hits with a rasengan, that's all.
If you don't believe this, compare Naruto before learning Rasengan to Naruto now. Remember how he defeated Neji and helped fight Zabuza. He was WAY smarter than he is now.