Abandoned Core Theme: The "hard work beats talent" message (Lee vs. Neji) is completely betrayed. Protagonists succeed due to destiny, prophecy, and inherited power.
Talk-No-Jutsu: A plot device where villains with complex ideological grievances are converted by a speech, often negating narrative consequences (e.g., Nagato, Obito).
Power Creep Ruins Tactics: The shift from strategic ninja combat to massive, DBZ-style chakra nuke battles makes 99% of the cast irrelevant.
The Final Villain Switcheroo: The perfectly built-up villain, Madara, is unceremoniously killed for a last-minute new villain (Kaguya) with zero foreshadowing.
Meaningless Death of Neji: He dies to reinforce a theme about "breaking destiny," which is immediately contradicted by Naruto and Sasuke being the chosen reincarnations of demigods.
Sharingan De-evolution: It evolves from a clever eye trick into a deus ex machina that can do literally anything (time travel, resurrection, perfect defense).
Poor Handling of Female Characters: Most are defined solely by their love for a man (Sakura, Hinata, Rin), with little independent agency or narrative purpose.
Illogical World-Building: The child soldier economy, village political structure, and use of Tailed Beasts as WMDs make no sense under scrutiny.
Forgiveness Without Consequence: Mass murderers (Obito, Sasuke) are forgiven after a sad backstory, facing no legal or societal repercussions.
Edo Tensei Breaks Stakes: The resurrection jutsu cheapens death, bringing back countless characters and removing emotional weight from the final war.
Repetitive Sasuke Cycle: His character arc is stuck in a loop: seek revenge, get power, lose, repeat. His final "revolution" plan is idiotic and lasts one chapter.
The Reincarnation Retcon: The Ashura/Indra plotline retroactively makes Naruto and Sasuke's struggle about destiny, not their own choices or merits.
Ineffective "Peace": The series ends without solving the ninja system's core issues. Boruto shows the problems (corruption, new threats) persist, proving Naruto's method was a band-aid.
Orochimaru's Absurd Redemption: The psychopathic, child-experimenting villain gets a slap on the wrist and is left to run a scientific lab, completely unpunished.
The Byakugan Is Obsolete: Introduced as equal to the Sharingan, it becomes completely useless and its clan's internal slavery plot is dropped.
Filler & Pacing: The anime is infamous for bloated filler arcs, and the Fourth Great Ninja War arc is a slog of revivals and flashbacks.
Logical Fight Inconsistencies: Characters explain their techniques mid-battle, power levels fluctuate for plot convenience, and established rules (e.g., substitution jutsu) are ignored.
Childish View of Politics: Complex issues of hatred, war, and governance are framed as problems solvable by one charismatic hero's sheer willpower, not systemic change.