1.)
Differences from Naruto's Rasengan summarized (I think everyone knows, and all have been posted, I'm just gathering them up.) For a visual comparison please see the link:
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a.) Kono's was much smaller indicating he can't draw out enough chakra or he can draw out enough, but not control it (thus he needs to draw out less).
b.) He required two hands (one his, one a shadow clone) to control the Rasengan
c.) It took him up to three years to learn it.
d.) He didn't have Jiraiya/Ebisu to help him, Ebisu didn't know Kono learned it. However during Naruto's training with Jiraiya, he was required to do the vast majority alone.
e.) This technique is as hard to land as oodama Rasengan, but it is much weaker.
f.) Konohamaru looks like he's a good/great Ninja (future Hokage, and I bet Naruto's apprentice later on), but he's not Naruto in my book. Naruto may be dumb about some things, but when it comes to learning/teaching(apparently) jutsu, he's legendary. Konohamaru's got a lot of potential, but he needs time.
g.) That weak Rasengan didn't kill the Pein body, and that's Kono's best jutsu, so I guess we get to see Ebisu? Or the Pein body will leave since he doesn't know, and another body does.
2.)
Pein: I think it's an assumption that Nagato's nearby. It was based off of the way Ino's clan technique works. Differences are that Pein uses dead bodies with chakra receivers, which may overcome that requirement.
b.) How the hell does the
most powerful eye technique miss a shadow clone, and start sucking it's soul out? If Pein isn't using the Rinnegan to control the dead bodies but the chakra receivers, does the Rinnegan still have that shared vision, or was that the real Pein watching the whole time? I'm trying to figure out what the Rinnegan does exactly.
3.)
Shizune: If she dies, who does all the Hokage work? Does Pein even know what the toad mountain name means? It's said to be impossible to find, and requires a month's travel by foot. I don't see how Pein is going to find him, Naruto will return a sage to a ruined Konoha, and fight Pein later.
4.) :naruto:
Naruto: Those saying he doesn't have any techniques that are special besides shadow clones and Rasengan are wrong. FR was forbidden, but as a sage he can pull it off. It was also incomplete, so we have yet to see it. He has some devastating jutsu that slices through trees far away. He now knows how to use shadow clones besides making them just run in blindly to their death (ex. Kakuzu fight). He will have sage mode down without fusion. I have no idea how much stronger that makes him, other than from what I saw from Jiraiya, he should be incredible. With sage mode he's learned toad taijutsu completely and sage techniques (not fully down according to Pa toad). Now that Naruto is at the point of making new techniques (tree slicer), he's going to make more signature moves. Finally, don't forget his summoning ability with the toads of course.
5.) :kakashi:
Kakashi: We won't know whatsoever about his status until Pein is gone and they're going over the damage to Konoha and the injured/dead. As mentioned this is classic suspense writing. We wouldn't still be talking about Kakashi like this if he was dead. Jiraiya died, and people still refused to believe he's dead.
*If you made it this far, you're a stud. Sorry it's so long
that spoiler! the manga seems to come out really good, i like it how Kishi made it end 
