You know, I was discussing the exact same thing with my sister - that Akatsuki was kind of killed off too fast. What would have been awesome if just like how Pain was the false leader of Akatsuki, Madara's Akatsuki group wasn't the "REAL" Akatsuki. This makes even more sense considering that hardly any of the Akatsuki members knew of who Madara was or what his goals were. The 'real/ Akatsuki would be the ones that know of Madara's actual plans, a group of 10 or 15 new, badass characters that could be leaders of platoons in the war. This would also flesh out why Madara is so confident in the pieces that has. The way it is now, it's almost like Akatsuki was an afterthought. For example, no one really is excited by Kakuzu's ability because it's like "been there, done that"
And yeah, I agree with you about the One Piece point and Impel Down. New characters, and they didn't even fight, but we know we'll be seeing them in the New World down the line.
About this, I feel the same way. I loved how Naruto came onto the scene, it was like exactly what I would have wanted in his reappearance. But after he got pinned down by Pains chakra rods, it went downhill from there. The fact that Naruto forgave Pain was truly annoying, but worst of all it took the weight off of Jiraiya's death completely.
This is one thing I'm iffy about - the comparison between how Sasuke feels for the one who died in his life and how Naruto feels. You know that with everything that Sasuke does post-Itachi's death, it is involving Itachi or for Itachi. Whereas with Naruto, you feel like everything he does...is for Sasuke. Not Jiraiya. Has Naruto even mentioned the Pervy Sage since the end of the Pain fight? What the hell is up with that?
Last but not least, the fact that Pain was on his high horse about "THE PAIN OF THE WORLD CAN NEVER END" and then 5 minutes later "Oh, I understand what you're saying, student of Jiraiya" and then resurrects the entire village (this was lame as hell too) made absolutely know sense.