1. That Sakura was the main female protagonist. I mean, what were you thinking Kishi?! Did you think we'd like a girl who couldn't contribute nearly as much as her teammates and whined about it?! She's just a character that filled a spot on the team 7 roster. Seriously, look at the Kaguya punching A-pull, and ask yourself, why did Kishi force such a thing? It's because she's the 3rd wheel that must be there for some reason. You know you screwed up with a character if the character's fails are like a running joke that's not supposed to be funny.
However, as much as I'm whining about that, part 2 Sakura, all things said, she wasn't that bad(other than immediately flirting with Sasuke again). Everything I listed was a mere annoyance I could generally overlook by focusing on Naruto, Sasuke, and Kakashi. It was still a thought though. However, what I truly hated was part 1 Sakura. One of the most annoying and hate-inspiring characters in existence for how she was nothing but Sasuke's little fangirl who puts down Naruto for no blasted reason! The fact that she refused to believe Naruto saved her from Gaara alone is enough to earn my eternal hatred for the character. What a B!
2. The 5 kage summit arc! Who boy! Why has no one ever mentioned this arc? Many jump on the hate train to say that the war series of arcs was the worst, but no, it's not. How should I say this? The war arcs had its fair share of nonsensical moments and potholes, but at least a lot of characters were done justice, and some of the best moments came from this arc. The 5 kage arc was the worst arc.
The reason why it's so bad is because Kishi took a huge knife, took Naruto and Sasuke's character, and then butchered them beyond recognition! He screwed up Naruto by making him have panic attacks over Sasuke. Naruto was made out to be pathetic that arc, which really ticks me off since we all know he's stronger than that! Hyperventilating?! Going flat on the ground begging for forgiveness for his friend's mess and not even coming up with a defense?! As a Naruto fan, I don't remember this arc fondly.
How Kishi butchered Sasuke. Ok, Sasuke was always the avenger. He had his outbursts, but Sasuke was always focused. You didn't see Sasuke going after the entire Akatsuki for Itachi. He just killed those in his way, or those that'd benefit his cause (attempt on Naruto). Whereas Sasuke's generally respectable, he was pathetically hilarious during this arc. He went absolutely nuts! Sasuke went to a focused killer to an absolute psychotic lunatic! He was trying to kill everyone for not knowing what Itachi did for them despite the fact that he wanted it that way. He basically was doing something terrible to the brother he claimed to love for self-gratification. I'm fairly certain 90% of the period jokes and emo portrayal of Sasuke came from this arc.
3. The fact that Kaguya had no backstory. The reason why Kaguya isn't a great villain is because she has no backstory. With a seeming goddess that can create entire realities with a power she stole, you'd think Kishi would give Kaguya enough attention to make us care, but he didn't. He talked about how she was good at first, but degraded, but he didn't show it. Kaguya could have been a great character. Someone with all the power in the world, but she couldn't solve humanity's problems. She had so much potential, yet Kishi somehow flopped it!
4. That peace seemed to have been achieved before Naruto became hokage. He became hokage recently, and already, we see a huge change. So, basically, the prophecy was thrown out the window in favor of the bench-warmer known as Kakashi. What was the point? Is this just fanservice gratification of Naruto fulfilling his dream, or is he supposed to be the light of the future? Kishi didn't leave any problems to give Naruto's hokage title meaning, and that's a pathetic disgrace to what Naruto went throughout the series.
Ok, I'm done ranting. I love pretty much anything else in the series, with minor things that I dislike.