1. I believe all could have been undone had the entire story of Otsutsuki's (Kaguya, Hagoromo, and Hamura) made just Lore and background. Meaning, cool- Indra and Ashura should've been people, but shouldn't have been linked to Naruto and Sasuke so specifically. I completely agree with you, that Naruto went from underdog to "the chosen one" almost and that does annoy me. The Black Zetsu scheme should've been kicked out completely, making Madara the master puppeteer in the long run and Madara with both Rinnegan and Ten Tails Jinchuuriki mode should've been the final boss for Naruto and Sasuke, and literally they could've done the same ending they did with Kaguya (the Six Paths Planetary Devastation), with Sakura contributing with overhead jab. Obito could've transferred his powers to Kakashi in a less spiritual fashion, and a lot could have gone right.
2. One issue that will always hinder Shippuden is the terrible filler placement. Kakashi and Itachi's respective backstory arcs could've been made into compelling OVAs (similar to what DBZ did with History of Trunks and Bardock, The Father of Goku) rather than cut out a solid 25-30 episodes in the middle of the intense storyline taking place. War was dragged on far too long.
3. I have a love-hate relationship with Sasuke's story. He embodies several key themes of Naruto, the obvious one is revenge, and I think the other one would be manipulation. The entirety of hardship that plays out in Naruto is due to manipulation done for your own benefit. (i.e. Madara > Obito > Nagato/Akatsuki). Sasuke throughout the story is manipulated by one cause or the other, and is never able to find his own path, and by the time he has the chance to find his own path (out of Orochimaru's grasp, learns the truth about Itachi), his road up till then has been so distorted, that he can't even make a logical decision. The arc between the defeat of Pain and the start of the war, where Sasuke is just running a checklist, fights Killer Bee, fights the Kages, and finally fights Danzo, threw his character development off significantly and I think hurt all the good things about Sasuke.
4. Kishimoto did not know how to make female characters whatsoever, with the sole exception being Konan, who I think was the one character written beautifully, as she is a true ride or die. Tenten, Ino, Shizune = irrelevant. Tsunade, the renown MEDICAL NINJA, can't handle the sight of blood??? Kurenai has a relationship and a baby and then gets thrown off the face of the Earth. Anko gets dogged by both Orochimaru and Kabuto with ease (and for some reason in the Boruto generation she is MORBIDLY OBESE. Temari is shown as strong and stubborn, but doesn't get to shine ever....Now Sakura - they started off Shippuden with good work. Has the drive to improve with Tsunade's mentorship, and with Chiyo's help, she takes down Sasori, who Deidara himself claims to be weaker and less experienced than. Perfect set-up for her. But then the series shows how Naruto was chasing Sasuke so hard, both to surpass him as a ninja and bring him back as a friend, and Sakura gives up quite easily. Hundred Healings Mark and War-arc Sakura should've not had such a huge gap between her Team 7 comrades. Obviously, I wouldn't respect it if she was Naruto/Sasuke tier, but they blatantly ruin her character at times where they shouldn't have. She hesitates to splice the Rinnegan Obito possessed, and allows Madara to finesse his way into the Kamui dimension. Against Madara, she didn't do jack but get piped with the rod, literally.
Overall - after Sasuke leaves, Jiraiya should've immediately took off with Naruto, and Part 1 should've been restricted to 150 episodes, and Shippuden shouldn't have had exceeded 350.





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