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It is very common for writers to change their original story. Often times when they believe it conflicts with past, present or future plot devices or simply because they disliked the original concept and wished to change it. Jean Grey was revived in the x-men comic as an official retcon six years after her death. How it happened was they changed the phoenix force inside of her from her own power to a cosmic entity that possessed her and took on her memories, appearance and powers after she died.
Madara's backstory came off as retconned to me. It is easily explainable by the Uchiha changing the story, but the fact of the matter is, originally, Itachi stated Madara was becoming badly sick and blinded by his MS and in an effort to save his own life, took Izuna's eyes and killed him, Izuna showing no sign of being fatally wounded as he was in the second flashback when Tobirama slashed him and Madara stated he was going to die anyway so he took his eyes to avenge him.
A second one is Naruto's small change after training with Jiraiya. I believe Kishimoto may have initially planned to make him stronger, possibly with sage mode, his own legendary weapon and another element, but believed it would have made him come off as too powerful and wished for Sasuke to look more powerful and unbeatable. Of course there really isn't a basis for this, it's just my hypothesis.
A third is the Hyuugas having little involvement in the plot in part 2. It's always bothered me. They had an ocular kekkei Genki like sharingan and Rinnegan, as well as a developed, and mysterious clan and two characters very developed and relateable to the main in part two, yet all of a sudden, they became secondary. Now we learn that Kakashi's theory was right and the byakugan originated in conjunction with the sharingan and rinnegan. I believe Kishimoto initially planned for them to be a larger part of the story, but changed it because he felt it was incoherent with other aspects and plots.
A forth is the Edo seven swordsmen and of the mist and Hanzo. The seven swordsmen were as legendary as the sannin. One was the original antagonist of the series and a driving character for the main characters while another became an Akatsuki, and one of the most powerful at that. Yet, when they made their epic appearance, they were seemingly off-paneled. This, in conjunction with mangetsu being revived as well and suigetsu never obtaining all the swords as he wished, felt fishy to me. I believe Kishmoto may have originally planned to give them a large part in the war arc and for sasuke, taka and several K11 to fight them, but was likely forced by his editors to cut them out, probably because they wanted him to get to the Obito, Madara and Kabuto fights faster. The same goes for Hanzo, who supposedly enacted the third shinobi war, was the tyrant of amegakure, make pain and fought and named the sannin, yet he was defeated by an old Samurai, with no jutsus and little to no development or relevance to the plot.
Madara's backstory came off as retconned to me. It is easily explainable by the Uchiha changing the story, but the fact of the matter is, originally, Itachi stated Madara was becoming badly sick and blinded by his MS and in an effort to save his own life, took Izuna's eyes and killed him, Izuna showing no sign of being fatally wounded as he was in the second flashback when Tobirama slashed him and Madara stated he was going to die anyway so he took his eyes to avenge him.
A second one is Naruto's small change after training with Jiraiya. I believe Kishimoto may have initially planned to make him stronger, possibly with sage mode, his own legendary weapon and another element, but believed it would have made him come off as too powerful and wished for Sasuke to look more powerful and unbeatable. Of course there really isn't a basis for this, it's just my hypothesis.
A third is the Hyuugas having little involvement in the plot in part 2. It's always bothered me. They had an ocular kekkei Genki like sharingan and Rinnegan, as well as a developed, and mysterious clan and two characters very developed and relateable to the main in part two, yet all of a sudden, they became secondary. Now we learn that Kakashi's theory was right and the byakugan originated in conjunction with the sharingan and rinnegan. I believe Kishimoto initially planned for them to be a larger part of the story, but changed it because he felt it was incoherent with other aspects and plots.
A forth is the Edo seven swordsmen and of the mist and Hanzo. The seven swordsmen were as legendary as the sannin. One was the original antagonist of the series and a driving character for the main characters while another became an Akatsuki, and one of the most powerful at that. Yet, when they made their epic appearance, they were seemingly off-paneled. This, in conjunction with mangetsu being revived as well and suigetsu never obtaining all the swords as he wished, felt fishy to me. I believe Kishmoto may have originally planned to give them a large part in the war arc and for sasuke, taka and several K11 to fight them, but was likely forced by his editors to cut them out, probably because they wanted him to get to the Obito, Madara and Kabuto fights faster. The same goes for Hanzo, who supposedly enacted the third shinobi war, was the tyrant of amegakure, make pain and fought and named the sannin, yet he was defeated by an old Samurai, with no jutsus and little to no development or relevance to the plot.