If it is all about chakra as your guys are saying we know that Naruto have enourmas chakra and thats why Jiraya learned rasengan.

I see only two reason to why his rasengan wasnt stronger than Sasukes chidori. One that he didnt put all of his chakra in it so he wouldnt kill Sasuke and we know that Naruto didnt want to kill him in the begining of the fight. Two that his rasengan right now is so weak or undeveloped that he cant put a lot power in to it.