Let me make one thing very clear from the start.
I like the Akatsuki.
They are a great group of villains with an interesting mix of personalities, goals, and abilities.
However, there is no doubt in my mind that mishandling them is one of the biggest sins of the manga.
Let's take a trip down the memory lane to a time when Orochimaru was the baddest of the bad. Kakashi had pretty much pissed himself at the thought of fighting him. He had his own village, and he even got to kill the Hokage, not to mention the part where he killed and impersonated the Kazekage for God knows how long.
He was a pretty big threat back then.
The introduction of Jiraya and Tsunade helped counterbalance things a little in the good guy's favor. However, Kishimoto found a way to turn up the tension again.
Enter Itachi and his trusty sidekick, Kisame.
Then we find out Itachi and Kisame are part of a group of nine S-Rank ninja.
So yeah, we were hyped back then.
The beginning of Part II saw the sudden introduction of the Akatsuki. Sasori and Deidara went into the Sand Village, beat Gaara, and walked out like bosses.
That was great.
The problem starts when Sasori dies at the end of that particular arc.
Let me rephrase that, Sasori, one of only nine members, dies in the same arc in which he is officially introduced. He is supposed to be one of the strongest ninja in the setting, yet he does not make it past one arc.
Oh, sure, we saw a bit of his character and really cool puppet tricks, but it was way too soon for a member of a group that had so much hype going for it to exit the stage.
And it's not going to be just him. Hidan and Kakuzu also die in the arc in which they are introduced. Deidara manages to last a bit longer but soon dies as well. When you stop to think about it, we ran out of Akatsuki at a frighteningly fast pace, and there is something that just doesn't fit there on several levels.
Before Part I ended, our heroes were fighting the Sound Five.
Now, I like the Sound Five (about half of them at least) and all, but their claim to fame is fighting two jounin who were nearly out of chakra and winning by using their Cursed Seal LV 2. That's the metric for their abilities and the stick by which we can judge the growth of our protagonists.
Are we really supposed to believe the good guys can now suddenly fight people who could bitch-slap Part I Kakashi after only two years? Yes, I know there were lots of things going on during those fights. Rather than a matter of power levels, it is the timing that's the issue here. It is still way too soon for Naruto, Shikamaru, and Sasuke to be beating people that good.
In a way, it's like we skipped a level. We never really get a taste of a fight between "normal" jounin-level opponents. We go straight to seeing the good guys fight it out with guys who make normal jounin piss themselves.
It'd have been really easy to give each Akatsuki a set of underlings. Hidan could have had random cultists. Kakuzu could have had hired mercenaries. Pain did have the entirety of the Rain village which ended up never doing anything important.
Anyway, we just needed guys who aren't as good as the real deal but still more than strong enough to give the good guys a run for their money, a sort of in-between stage. It'd have highlighted how strong the Akatsuki are and how much further the good guys needed to go.
Instead, we are forced into sudden elimination matches straight away.
By the time the war arrives, we have pretty much run out of bad guys to fight. It's only thanks to the most masterful use of necromancy ever, that we are able to have the roster filled again.
This is one of the moments in the manga (and not the only one) were going slower could have helped it massively. The conflict with the Akatsuki had a lot of set-up going for it, and there is nothing wrong with taking the scenic route every now and then when it comes to writing.
Taking time with the Akatsuki would have allowed us to see more of the Jinchuuriki they were hunting, and that'd have been really cool.
We could have had Konoha reaching out to other villages, and Naruto meeting his fellow Jinchuuriki one by one as they faced against whatever Akatsuki was throwing at them this particular time. It'd have also offered a chance to gradually introduce the other villages instead of just showing them all at once for the Kage Summit.
That didn't happen so this is Sin #4.