when the so6p split up the kyubi, he knew that the nine tails would be the strongest. and whoever could control him, he knew would have to be pure of heart. So he put alot of his chakra in the nine tails to be used when it could be controlled. he probably did it just in case something like what madara's doing would happen. That's my theory as to why Naruto looks the way he does. There were other things in my theory but i'm hungover and forgot.