The Naruto franchise begins with Orochimaru as its main villain, but over the course of the story, it's clear that he's not the only bad guy the main characters need to worry about. The Akatsuki, with their quest to boost their own power and take over the world, becomes the bigger threat.
They might have stylish robes and fun characters, but the Akatsuki are kind of a mess as a secret organization of villains. There's a lot about the group that isn't cohesive, from their tendency for backstabbing and each member having their own selfish goals to their actions not always lining up with what they say they want. To put it simply, the Akatsuki doesn't always make sense.
10 The Akatsuki Features A Power Imbalance Amongst Members
It's implied in the franchise that the Akatsuki seeks out shinobi who are the most powerful and the most ruthless for their ranks. The group wants people easily swayed to their side, sure, but they also want people who are going to be impossible to defeat. That's why the imbalance in abilities is so strange.
Zetsu, for example, doesn't have much to offer the group beyond his abilities for tracking. That's definitely a useful skill, but it's not on par with Hidan's near-immortality in a fight or Orochimaru's vast variety of skills.
9 Nagato & Konan Sought Out Obito After Yahiko Turned Him Down
Nagato, Konan, and Yahiko, the three children trained by Jiraiya after the Third Shinobi World War, are the founders of the Akatsuki. When Obito seeks them out himself, wanting to join for his own selfish reasons, Yahiko turns him down. He knows that Obito doesn't share their same goals.
Nagato and Konan, who keep the Akatsuki going as a way to honor their fallen friend, then immediately seek Obito out after his death. It's odd that they would do this despite knowing Yahiko's reasons for turning him down in the first place.
8 Konan's Abilities Are Uneven
Konan has a lot of interesting abilities in the series, but the most notable one is her control of paper. She uses it as a weapon, to augment her appearance, and even to give herself wings. That being said, some of her means of defense with it don't make any sense in the context of Naruto.
She uses paper to shield herself from a fire-based attack from Jiraiya. No matter how powerful she is, the paper should burn. Naruto frequently uses nature releases to match opponents in power level, and real-world rules typically apply. That battle also doesn't make sense because Konan has an affinity for Water Release as well and could have just used water against Jiraiya's fire.
7 Naruto Talks Down Villains Who Have Been Working For Decades
Naruto's talk-no-jutsu is a thing of beauty in the series. That's because it's nearly unstoppable. It seems like he can talk anyone into or out of just about any action he wants as long as he's passionate and persistent.
This doesn't entirely make sense when it comes to his confrontations with the Akatsuki, however, Naruto manages to appeal to the humanity of both Obito and Nagato, which is admirable, but both of these characters have been following their paths for decades with no remorse. Obito is even often amused by his own cruelty, unlike Nagato. Naruto being able to talk them both out of their plans doesn't seem likely.
6 Itachi's Plan & Sacrifices Had Flaws
Itachi is a fan favorite character because of the sacrifices he makes in his own life for Sasuke. The trouble is those sacrifices don't make a lot of sense. He wipes out his entire family and saves Sasuke, in hopes that Sasuke will one day become the village's hero.
Itachi also, however, still loves the village that betrayed his family. He also cares deeply about his brother. That doesn't stop Itachi from abandoning them both and joining the Akatsuki when he has no intention of carrying out their plans.
5 The Akatsuki Begins As A Path To Peace But Turns Deadly
The trio of friends from Amegakure who form the Akatsuki just want world peace. It's a lofty goal, but after seeing the ravages of war firsthand and training under Jiraiya, all they want is for no one else to go through what they went through.
That's why their plan is off-base. Pushing fear and literally murdering people who disagree with them is not a way to foster peace. It just leads to more fear, anger, and fighting.
4 The Akatsuki Is A Front For Collecting Tailed-Beasts
When Obito effectively takes over the Akatsuki, his plan is to use the group to collect the shinobi world's tailed-beasts and use them to take over the world himself. While that's a complicated plan on its own, this particular path doesn't line up well for the rest of the group either.
While Obito mostly stays in the shadows until he comes out as Tobi, the rest of the group puts their lives on the line for his plan. They don't appear to be particularly adept at catching the tailed-beasts, so it's strange that no one tried to find a better approach to taking over the world.
3 The Akatsuki's Partnerships Often End In Murder
There is one very harsh reality the members of the Akatsuki have to face: they might not survive their teammates. The group is paired off for missions in much the same way Konoha creates three-person shinobi teams. Not all of those partnerships work out.
Kakuzu is the best example of this. He's known for killing his partners when they annoy him, so it's odd that the Akatsuki doesn't just get rid of him completely and find a new pair of shinobi better suited to their goals. It can't be good for morale when someone keeps killing members of the ranks from within.
2 The Ideologies Of The Members Don't Match Up
If there's one thing evident to the audience after spending just a few moments with the members of the Akatsuki, it's that everyone else is there for their own selfish reasons, and the group is full of potential traitors. When Orochimaru joined, he just wanted to further his own power. Nagato and Konan really do want world peace. The rest, however, can have more complicated ideas.
Obito specifically wants revenge on Konoha, but he also wants Pain's position in the group. Itachi is a double agent of sorts, not wanting the Akatsuki to actually achieve their goals. Zetsu wants to bring Kaguya back to power. When so many of their motivations don't line up, it no doubt makes it harder to take over the shinobi world together.
1 All Of The Akatsuki Recruits Are Missing-Nin
There is one thing everyone in the Akatsuki has in common: they all reject their home villages and become missing-nin. Missing ninja are fugitives, seen as people who essentially commit treason against their governments. That means they all have to keep a low profile, no matter how much Deidara likes causing a scene.
It might have been more effective for the Akatsuki to recruit sympathizers who aren't fugitives, or to not force people to leave their village behind. If the organization actually had plants in the various villages, they really would have known everything going on and their quests would have been a little easier.