I'm not sure if these reasons were listed already, but I had some issues with other things in the manga besides the flow of the story, plot holes galore, and other inconsistencies.
One main issue I had was the villains. I do not mind redeeming people, since second chances seemed to be one of many themes in the manga. However, I would have liked some variety, such as villains that were just plain evil and irredeemable. Another issue I had with this particular thing is that Gaara was the only "villain" that was redeemed and given a chance to truly change his life. Every other redeemed villain was killed off shortly after. I don't really count Sasuke, since he was a MC. (I never thought he was going to be killed off, even with the prophecy of the Old Toad Sage.) Then, there was Kabuto and Orochimaru. I did not like how they were the longest main villains in the story, only to fall incredibly short at the end.
I did not like the shallowness of the characters. For a manga about bonds and love, it fell short. Throughout the manga, I continuously got the message that Kishimoto does not know what love is or how to form real bonds. Most people do not end up with the crushes that they had as a child. Sakura, and even Hinata, were made to be completely stupid the entire series for "loving" someone who did not look at them twice until the very end when Kishimoto trolled us with fan service. People who really love others do not become doormats to be walked all over, ignore terrible character flaws, and/or have no standards or respect towards themselves. If you don't respect yourself, why should anyone else? Also, according to Kishimoto logic from this manga, obsession is a passionate form of love. WRONG! Obsession is an extreme form of lust. Obsession towards other humans is dehumanizing.
The whole bond aspect is also flawed. I never understood how Naruto would call someone who tried to kill him and his other friends a best friend. I never understood how Sakura would be "in love" with someone who tried to kill her. I never understood how Naruto could consider Obito the coolest person, when he was the reason behind everything in the series, pretty much. It makes me wonder what kind of friends/significant others that Kishimoto has had to think these are healthy bonds.
Another thing I had an issue with was the misogyny. No woman in this series was very significant, even if her position or clan affiliation should have suggested otherwise. One prime example of this is Hinata. She is the clan heiress. She does not have the bird cage jutsu on her byakugan. Yet, she was never a match for Neji throughout the whole series. How does that make any sense? Of course, Sakura could have been handled much better, as well. With all her advancements of the jutsus that she learned, I was hoping for a plot twist that she was a Senju or something. My thought grew a bit more when her mother was shown to have incredible strength, as well. Another example is Tsunade. The whole arc with her and Madara was ridiculous at best. The "weak woman" crap really took away from the enjoyment of the battle. In real life, there are women who are better at many things than men, and there are men who are better at things than women. These things do not always line up with our gendered perceptions of how things "should be" either.
My last and biggest complaint of the entire series is the Senju. I understand that Kishimoto is a fanboy of the Uchiha clan, but part of that story had the Senju. We know the Uchiha were massacred. We know that the Uzumaki were killed during the Second War, so where are the Senju? They just mysteriously vanished without a trace, besides Tsunade. I want to know their story, as well.
Overall, I liked the manga. I just wish I wasn't left with a bunch of questions with no answers. Also, I wished that the characters of this series were handled better.