1.) Naruto vs. Pein is going to be epic. It's got to be longer than Itachi vs. Sasuke since Pein is currently sharing the top villain spot with Madara. Also, Madara might be like Pein in that one needs to know his secret to defeat him.
Also, I'd like Naruto to have an idea about Pein's secret due to Konoha research, but not actually know it in its entirety when they fight, but rather discover it completely as they fight.
Anyway, 20-30 issues of Pein vs. Naruto? Is that too much?
2.) With respect to Pein and Konan. They have two possible scouting jutsus we know. Pein's rain jutsu, but I think that that would be kind of obvious to Konoha since Pein is from rain country I think and also it probably has chakra in it, which someone like Kakashi or Neji could see.
The other jutsu is Konan's paper dispersal jutsu, but if she doesn't find Naruto, I'm not sure what Pein will do. I don't think that he alone can defeat Konoha, simply because he would run out of bodies. We also don't know how valuable each body is to him, or if they are simply vessels that can be replaced with a new one. Are they blank slates he fills in, or more like human puppets that Sasori uses?
3.) Naruto's jutsu and appearence after he returns after mastering senjutsu.
I will only list 3 jutsu, since that's a lot:
a.) one 4th Hokage jutsu or variant - everyone wants flying thundergod, but maybe they'll actually complete that jutsu inscribed on the toad. - probably an offensive short range jutsu.
b.) one toad jutsu with additional summons - i.e. stomach + toads - this will be his absolute defense jutsu
c.) at least one Naruto jutsu that he creates or extends an existing one to be his own - this is going to be his long range jutsu and utilize shadow clones. How funny would it be if he made a jutsu for defense called " clone sacrifice." He would surround himself with clones, like a dome, when he's about to get nailed and they take the blow for him. ( not gonna happen

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d.) If he can see nature chakra he shouldn't see it if he's in genjutsu.
e.) since he and Sasuke will fight, he needs something to stop Kirin and Ameratsu which are instant attacks, to which I only know of Susanoo to stop them.
Naruto can't just be as good as the pervy sage Jiraiya, just like Sasuke couldn't be just as good as Lee against Gaara. So expect him to whip out a badass jutsu that won't be seen at all until Pein and Naruto fight.
Appearance:
a.) He now carries a scroll like Jiraiya did that contains the contracts to summon the toads.
b.) He will keep the Konoha forehead protector
c) His uniform will be simpler and less reflective of his genin years than his previous one. This uniform needs to reflect his shift towards maturity but also his role as a toad sage and Konoha elite ninja. (Suggestions please!)
d.) I don't know about a new weapon, I suggested one that was cool, but what's listed above is a lot, so I don't want to overdo it. I'm interested in what others think because I'm kind of limited at the moment. Something wind, rasengan, or nature chakra could combine with.