Just want to clarify something here... no matter how much of Naruto's chakra gets sucked out of him, he can just regenerate a close to infinite amount with the kyubi in him, right?
On note of the story, I think people will be disappointed no matter what happens. We will get a bunch of redundant boss fights where naruto and bee will either a) blow through everyone or b) have some trouble but quickly end it anyway, until the final madara/sasuke/naruto/kabuto battle where all hell breaks loose.
There's a long way to go with this redundancy thing haha
As for Pain loosing so fast... there's no other explanation other than Kishi's fan service with itachi. Imo, this fight should have at least taken 6 chapters. But what can I expect when the development of the story is so poor
