Just talked about this so here's something I cooked up.
Akatsuki should not have become the focal point of part II until later on. Instead they should have made showcase appearances, and Naruto with others should have had to deal with them as they interrupted whatever was going on.
For instance here's a cool way to introduce Hidan and Kakuzu.
Let's say Team Kakashi and Team Kurenai were sent on a mission to retrieve some ancient artifact from some ruins. This artifact is valuable, and is also capable of being used for other purposes....let's say maybee speeding up Jutsu (like the Bijuu extraction Jutsu). So as they go after this artifact, Orochimaru send his henchmen after it in an attempt to ready his body faster to take Sasuke/deal with his arms.
So upon discovering it, The Konoha team and Orochimaru's team (a nice way to introduce more groups like Guren's team) begin to clash...after a good bit of fighting, all the sudden Akatsuki crashes the party and takes the artifact....and they don't even reveal their names. You just see these two guys show up, put a little beat down on people and take off just like that.
This would have done several things.
1. Kept the thought of Mystery in Akatsuki instead of who's getting foddered off next.
2. Would have left us asking, "who the heck were they?" Once again adding to mystery and the thought that Akatsuki really was crazy strong.
3. Would have allowed for a more creative and longer story. That way we still had Konoha operating on the ninja missions system instead of it just becoming a never ending cycle of shuffling through Akatsuki.
4. Kept Akatsuki around for a lot longer....and had they declared war without showing all of their true strength....it would have been that much more intense when Zetsu armies and Edo tensei had been added to these mystery monsters we hadn't entirely seen yet! Imagine Kisame leading the assault on the lightning coast and Hidan and Kakuzu taking it to the Second Division's Taijutsu users!
Yeah we needed more Akatsuki
