The Fourth Great Ninja War is the biggest arc in Naruto, and spans over half of the second part of the story. The war was triggered by Kabuto Yakushi and Obito Uchiha, who sought control over the remaining Tailed Beasts in order to complete the Project Tsuki no Me.
To counter this threat, the Five Great Nations banded together and formed the first Shinobi Alliance. While the war arc is filled with tremendous battles and some of the most incredible moments in the anime series, it also has its weak parts, and some of them don't make much sense at all.
8 Kaguya's Revival
Kaguya Otsutsuki was mentioned by Hagoromo Otsutsuki for the first time towards the end of Naruto. Just a few chapters later, she made her return and suddenly became the main villain of the story. While she was certainly strong, fans simply couldn't turn a blind eye to the fact that her presence in the war made very little sense.
To make matters worse, Kaguya Otsutsuki's revival came at the cost of Madara Uchiha, who had been built up as the main antagonist for years. This sudden change in direction was a bit jarring.
7 Very Few Major Characters Died
The Naruto world saw a total of four wars break out over the years; however, the scale of the first three wars was certainly not comparable to that of the Fourth Great Ninja War. While the first three wars were quite dangerous, the fourth saw the world face the biggest threat in history. Despite creating a Shinobi Alliance, the ninja villages were on the back foot.
Surprisingly, though very few characters who actually mattered died in the war. Apart from those who got caught up in the blast at the HQ, the only major character who died on the side of the Shinobi Alliance was Neji. The rest all seemed to have heavy plot armor.
6 The Main Villains Were Turned Good
Masashi Kishimoto, the creator of Naruto, has a habit of turning every villain good. Clearly, this took over during the Fourth Great Ninja War as well. The war started with Kabuto Yakushi and Obito Uchiha against the world, by the end of it, both of them were helping the Shinobi Alliance in a war that they had started in the first place.
Neither Obito nor Kabuto had to face any consequences for essentially butchering people by the thousands, which makes little sense. In fact, towards the end, even Madara was painted as a character who was misled by Black Zetsu. This could well be the worst writing decision made by Kishimoto in the entirety of the story. Redemption arcs for villains can work, but fans disliked the lack of repercussions.
5 Orochimaru's Change Of Heart
Orochimaru was another villain who eventually turned good in the war. While his role in the series had already dwindled by then, at no point did he show any desire to help Konoha.
His personal goals always took precedence over everything yet in the end, he chose to help Sasuke. Later, he even helped those fighting in the war when he had no reason to do so. What's even worse, Orochimaru was turned into comedic relief, which was incredibly sad given how much potential he carried as a main villain.
4 Obito's Survival
Obito Uchiha's eventual rise towards becoming the next Madara wasn't random. Kishimoto carefully planted the seeds for it years before the reveal was official. In the Third Great Ninja War, Obito was presumed to have died after being crushed by a rock.
However, in the Fourth Great Ninja War, his backstory was told. It was revealed that the rock accidentally phased through half of his body before Madara eventually saved him, which is eerily similar to how Kamui works. Strangely enough, this shouldn't have been possible, as his Mangekyo Sharingan hadn't awakened at this point. In fact, his regular Sharingan wasn't even close to maturity. Obito should never have survived in the first place.
3 Madara Breaking Edo Tensei
As Itachi helped cancel the Edo Tensei, countless people who Kabuto Yakushi had reanimated were finally freed from their shackles and went back to enjoying the afterlife — except for Madara Uchiha. Surprisingly, Madara knew how to break the Edo Tensei and severed his connection with Kabuto to continue existing as a reanimation.
This made absolutely no sense as Tobirama Senju, the creator of the Jutsu, never used that jutsu. Tobirama faced a dire situation where he would ideally have wanted to sever the connection to the caster; however, he chose to never do so.
2 Kakashi Getting Obito's Chakra
Very few plot details made sense towards the end of the Fourth Great Ninja War, especially the fight with Kaguya Otsutsuki. As if the sudden appearance of an alien goddess wasn't enough, Kishimoto decided to give a Kakashi rather bizarre power-up.
After Obito died, he chose to return from the land of the dead to give Kakashi his chakra for a few minutes. This helped the latter use Six Paths powers, along with a mighty Susano'o, which eventually played a massive role in ending the war. This event definitely came from out of nowhere.
1 The Way Neji Died
More characters should have died in the Fourth Great Ninja War, but the only one who ended up dying was Neji. To make things even worse, Neji's death was handled in a senseless manner. During the climax of the war, the Ten-Tails started unleashing a barrage of Wood Release jutsu, which struck countless people.
To protect Naruto, Hinata jumped in its path, and to save Hinata from a horrible fate, Neji chose to give his life up instead. For two characters who had the Byakugan, seeing through incoming projectiles should have been incredibly easy. What's more, even if they didn't see them all, Hyuga techniques such as Kaiten would have effectively dealt with anything the Ten-Tails threw this way. Neji had no reason to die.