Madara is arguably the best villain within Naruto, with a large portion of fans claiming there's no other villain quite like him in all of anime. He might be considered the "big bad," but he's not actually the final boss of Naruto: Shippuden. Of course, that role was given to Kaguya, the founder of early ninjutsu that would later turn into the plethora of jutsu fans know in the current world of Naruto.
Yet, Madara is still the better know villain, with most of the show's plot centered around his goal: to encompass the entire world within an illusionary system in which everyone could live happy and free of pain. So, one could argue that Madara was the better villain and should've been the final one within the show instead of Kaguya.
10 Kaguya Wouldn't Have Been Revived
This might be a no-brainer, but when making a shift like this within a series, one must consider the events that consequently wouldn't have happened. Sure, Kaguya wouldn't have been revived, but writer Masashi Kishimoto might have still included her in the story with a different role. If she wasn't the final villain, Kishimoto probably would've kept Kaguya a myth and lessened her overall impact.
She would have remained nothing but a tale about the beginning of the shinobi world and the audience probably wouldn't have learned much about her other than being the mother of the Sage of Six Paths.
9 Madara Could've Been The One Sealed In The Moon
If Kaguya isn't around, the question immediately shifts to how Madara would be defeated. Well, it's easy to assume that Naruto and Sasuke would defeat the enemy in a similar way to how they sealed Kaguya in the moon. Or, perhaps they'd find a way to somehow turn Madara to the side of good or beat him outright.
Either way, defeating Madara in an alternative way seems unlikely after Madara defeated the five current Kage with little effort, and proved to be more than a match for the rest of the shinobi world.
8 Madara Could Still Be Alive
Assuming Zetsu didn't stab Madara in the back, Madara could still be alive. After being completely revived, Madara could have somehow joined to Naruto's side because of some out-of-left-field plot twist and have potentially been seen returning to the Hidden Leaf.
And if Madara had been hypothetically sealed in the moon, it would be interesting to see in Boruto if there were a couple of scenes where his consciousness almost leaked from his prison, giving Naruto and Sasuke visions of his return.
7 Everyone Might Have Been Trapped in Madara's Infinite Tsukuyomi
A victory over Madara seems like a bit of a stretch considering how powerful the enemy appeared in the concluding arcs of Shippuden. It's not a stretch, however, to imagine Madara winning against the five main shinobi villages. With Madara winning, the world inevitably would be caught under his genjutsu, resulting in everyone living in an illusion of happiness as they would live their lives in complete and utter peace — or so Madara claims.
In fact, this is already theorized by fans to have happened, suggesting that the newest installment focused around Boruto takes place in the Infinite Tsukuyomi.
6 Obito Might Have Survived
When Gaara lost the One-Tailed Beast Shukaku, the viewers were told there wasn't a way to save him, which ended up being overturned when Chiyo sacrificed her life in exchange for Gaara's. So why couldn't Obito also be saved? Well, saving Obito after losing the Ten-Tails might be a tad different because of the potency of its power. Another interesting thought would be resealing the Ten-Tails in him, taking the burden of making sure no one reawakens it again as Obito exiles himself from humanity.
Either way, Obito ended up dying as a result of the Kaguya battle and lasted a long time without the Tailed Beast due to Zetsu. He lived longer than he should have to begin with, plus, it's fun to think of a way the character could've theoretically survived the war with the Ten-Tails or multiple tailed-beasts' chakra within him if Kaguya didn't kill him toward the end of the anime.
5 Kakashi Might Have Kept His Sharingan
Branching off from Obito somehow surviving the war, it's also possible for Kakashi to have kept his Sharingan. The only reason Kakashi was able to use the powerful eye was because Obito gave it to him as a gift, containing a portion of Obiro's chakra. However, Madara stole that eye from Kakashi at the end of the war, leaving Kakashi without the Sharingan. Then, after a series of events, Obito dies and gives Kakashi the power of the Sharingan back (because plot), but Kakashi would use up the chakra from Obito, losing the power once again.
So, if Madara was defeated, it'd be possible for Kakashi to get his eye back. Alternatively, if Obito survived, Kakashi could have received more chakra from his childhood friend, giving him the power of the Sharingan for the third time in the series.
4 Zetsu's Existence & Purpose Would Be Rewritten Completely
This is where it really starts to get theoretical. Once again, if Kaguya wasn't the final villain, many of the characters' roles and influence would change since Kishimoto would have made different creative decisions with his characters. One of the most notable characters who would have had a role change was Zetsu.
Would Kishimoto still have him try to kill Madara but fail? Would Zetsu just be another pawn in Madara's plan and a result of another experiment? Would Zetsu even exist at all? These are all questions fans need to acknowledge when thinking about a world in which Kaguya wasn't the final villain.
3 Naruto & Sasuke Might Not Have Met The Sage Of Six Paths
Another character who might have been altered greatly was the Sage of Six Paths. Without Kaguya being the final villain, Kishimoto might not have included the whole "sealing in the moon" aspect. He might not have thought of it, or maybe he would have simply chosen a different way to fend of Madara.
In either scenario, it's fair to assume that Hagoromo never would've met with Naruto and Sasuke if Kishimoto never intended to revive Kaguya. In that case, Naruto and Sasuke wouldn't have gained the powers of the Six Paths
2 Might Guy Could Be Dead
In a world where Naruto wasn't gifted additional powers from Hagoromo, Might Guy would have definitely died, assuming he still unlocked the Eighth Gate of Death. After Guy finished his battle of distracting Madara, he was nothing but a charred corpse slowly disintegrating into the earth below.
Naruto of course would use the power just gifted to him from Hagoromo to heal the man recently deemed the best taijutsu user of all time, halting the process of a slow death. Sure, Guy is still horribly injured from the battle, but it's better than dying.
1 The Anime Would Have A More "Complete" Ending
It's no secret that Kaguya's appearance is a bit sudden and out of nowhere. Everything Naruto and Sasuke had gone through was centered around the Akatsuki's plans, with Sasuke chasing after Itachi and Naruto being hunted due to the Nine-Tails inside him. Madara was the villain hyped up for hundreds of episodes and fans were fully invested in the character, ready to see him take on the countless shinobi of the modern world.
Madara's death is also sudden as he was stabbed in the back, which many would argue underscored the character. So, without Kaguya, would the ending of Shippuden be more complete, organized, or perhaps better? Many fans would say so.