Naruto's Fourth Great Ninja War was its biggest and most intense arc as the Five Great Nations joined forces to protect the Eight and the Nine-Tails from falling into the hands of the Akatsuki and stopping the Tsuki no Me project. The war saw the formation of the first Allied Shinobi Forces battle a combined force of Obito Uchiha's Akatsuki and Kabuto Yakushi's force of reanimated shinobi.
At the beginning of the war, it was established that Madara Uchiha was the main enemy of the Shinobi Alliance and Kabuto Yakushi was the guy who was backing him. Halfway through the war, however, things took a drastic turn as not only was Kabuto Yakushi defeated but the masked man was revealed to be someone else entirely and the real Madara Uchiha was brought back using Edo Tensei. With Obito Uchiha and Madara Uchiha now being established as the main enemies, the story headed into its final phase and surprised the fans with what is considered to be arguably one of the worst plot twists in the entire Naruto series, the revival of Kaguya Otsutsuki.
The Madara Uchiha Conundrum
Before diving into why Kaguya Otsutsuki's revival was not a great writing decision on Masashi Kishimoto's part, fans need to understand the importance of Madara Uchiha to the Naruto series. Naruto Shippuden began with Kurama mentioning Madara Uchiha upon seeing Sasuke. Immediately, it was established that Madara was a legend of the olden days and one who everyone needed to be wary of. With Obito declaring himself to be Madara, once again, the story indicated that he was, in fact, the main antagonist of the series. Having been a rival of Hashirama Senju and a man worthy of taking the era by the scruff of its neck, Madara Uchiha was a menace to the ninja world. Just like the many villains of Naruto, Madara wanted the same thing as the main characters of the story — peace. While Hashirama went his way to establish long-lasting peace, Madara decided to follow his own path, even if that path required him to bloody his hands.
By manipulating countless people, killing the likes of Rin, and even causing the greatest war in the history of shinobi, Madara was quite easily the greatest villain in the story. With his return in the Fourth Great Ninja War, it was quite evident that the final battle of the series would be one where Madara Uchiha would be taken down. Yet, in the most anticlimactic manner, Madara was struck down by Black Zetsu of all people and turned into a host for an alien parasite, Kaguya Otsutsuki. With a few strokes of his pen, Masashi Kishimoto killed off the greatest villain in Naruto, possibly because he didn't know how to deal with him, something that he admitted to himself.
Why Kaguya Otsutsuki Was A Bad Addition To The Story
Kaguya Otsutsuki's addition to the story is generally disliked by most Naruto fans for a plethora of reasons. For an endgame enemy to make sense, the author needs to establish a proper buildup for the villain to eventually take the stage and then for the heroes to fight them. Kishimoto himself accomplished this on several occasions in the story with the likes of Pain, who was first teased towards the end of the Sasuke Retrieval arc.
Later, throughout Naruto Shippuden, Kishimoto, once again, did a phenomenal job in building up to the fight against Pain. Similarly, Sasuke's fight against Itachi was rooted in the tragedy of the Uchiha clan and something that fans knew would inevitably happen. While this certainly doesn't mean that Kishimoto needed to foreshadow Kaguya Otsutsuki hundreds of chapters ago, it does make her addition to the story look much weaker compared to the rest.
It wouldn't be a stretch to say that Kaguya being revived all of a sudden was a move made for shock value, even though towards the end of the war, Kishimoto tried his best to drop hints about her eventual arrival through Hagoromo Otsutsuki.
What makes Kaguya's addition to the story even worse is that she took the spotlight from Madara Uchiha, who was already established as the greatest villain in the story. Just like the many villains of the Naruto series, Madara fought for peace in his way. While his way was certainly not perfect, fans had already made peace with the fact that was going to be the final enemy. After all, Madara did have a fantastic build-up to this point in the story.
Kaguya's arrival not only completely shattered any chance of the highly anticipated fight against Madara Uchiha but also gave fans a very bland and aimless villain. Kaguya, being the progenitor of chakra on earth, wanted to take back all the chakra from everyone once again. She had little to no care about the shinobi world and simply felt way too disconnected with the history of the shinobi and even the Fourth Great Ninja War itself. There is no denying that Kaguya was several times stronger than Madara Uchiha, however, her motivations, as a villain, were weak. Fans couldn't connect with her nor feel intimated by her the same way as they did with the likes of Madara Uchiha, Obito Uchiha, and even Pain.
The addition of Kaguya Otsutsuki might've been received better had Naruto made it clear that an alien species would be the final opponent that the shinobi world would face, however, that never happened. With Naruto's sequel, Boruto, having continued with the Otsutsuki alien plotline, it seems likelier than ever that Kaguya Otsutsuki was simply there to ensure that the franchise had a future beyond Naruto.