Itachi going from a genocidal maniac, and instead turned into a "good guy all along".
Sasuke becoming the main driving force behind the story instead of staying as, and developing into a better villain character.
Sasuke's cancerous relationship with Naruto and Sakura turning both into crying weakleakings during key moments of the story.
The War Arc.
Madara being built up as a genuis powerhouse and a genuine evil person, only to be turned into a man who was tricked by an ancient Goddess.
Orochimaru is really a good guy in the end! ... wait what? Yes that's kittening canon!
Every intersting character who died, and those we didn't know about but only hear about, all come back to life instead of Kishimoto just relying on the cast of character he already had built up.
Sasuke decided to try to assissnate the leaders of all of the villages.... nothing comes of this in the end.
Sasuke becoming a "good guy" again at all is ridiculous. That he was never punished and in the end was reward with Sakura is disgusting.
Women are mostly turned into trophies in the end. Their value, and how "succesful" of human beings they are ends up ammounting to "Did they get the D from the guy they wanted? Or did they have to settle for someone else?" Which basically means in Kishimoto's eyes Ino is a failure as a person.
Except for Hinata who gets her man because when you got kittens like her's, kitten get's done behind the scene thanks to SP. Which in reverse turns Naruto into her reward for all the positive things she did in the story. I mean seriously she didn't forget to say Naruto-Kun once, and I know Pokemon has made repeating one word over and over look easy but trust me it's not.
The realization that evey major conflict in human history since the whole "people can use chakra" thing happened, ended up being about one thing in the end. Bringing back the Rabbit Goddess..... since Black Zetsu was pulling all the strings from the beginning. The ninja system wasn't the problem at all. Humanity has no weaknesses in the level, they only can get tricked into being bad.
The ninja system stays around despite the fact that there is supposedly no need for warriors anymore. Despite this child soilders is so ingrade in their culture that parents expect their kids to die if need be, even though the village system is now set up for constant peace.
The evil that is a part of the human condition is brushed aside as not mattering. Everything from murder, slavery, indebted servitude, genoicde, human experimintation, and a system that doesn't value free will is rewarded in the end. No one is punished for their actions, and Kishimoto even tries to make it look like Madara wasn't really a bad guy in the end.... what what what?!!?!?
The tailed beast and the Sage even existing. Originally it was just the nine tails.... and then the demon that was inside Gaara was said to be "like the nine tails".... later we find out that these "tailed beast" are a part of the ninja system. We then also learn that Naruto's mother also had the nine tails inside her, yet with all this information gathered rereading early part one doesn't make any sense. Why the hell would people think Naruto IS the demon fox when eveyone knows that these beast are simply put into host bodies in order to portect the villages? People may not like them, but the Leaf village canon wise is shown to accept the host since they all loved Naruto's mother and where happy that she was the first lady of the leaf..... then like two weeks later after the fist couple is murdered the leaf turn against the new host..... despite the fact that they should all still be used to it to an extent and all should have a reason to take the 4ths request that Naruto be seen as a hero more honestly. Instead Naruto is thrown aside... why?
For some reason no one bothers to tell Naruto he is basically the son of the most famous couple of the Leaf who died for him. For no apparent reason. Why didn't the Third just say "Ladies and Gentleman the 4th and his wife gave up their lives in order to protect the village. Before they died though they were able to give life to their child, and then had to make a terrible choice. They decided to place the beast inside of their new born in order to protect us. Which means it is the job of this entire village now to make sure their child is raised correctly under the ideals that his parents lived and died for." Instead we got "This is the new hero kid...respect him." and for some reason the rest of the ninja village decided to forget about the world they live in, and just hate Naruto.... why?
Why? BECAUSE THIS STORY WASN'T PLANNED OUT FROM THE START! despite the claims of the pro ending fanbase.
Along this line the quesiton of how Jiraya and Kakashi didn't figure out that Naruto was the son of the 4th makes even less sense. If they knew before hand that he was his son makes it even worse! It means that two succesful career driven men, who cared about his parents, allowed their son's formative years to be lonely and broken. They latered showed they had no problem becoming father figures to Naruto, so why the hell did they wait so long to teach the kid that he could be loved?
Since Itachi was changed from homicidal murder into loyal solider of the leaf, it did two things that still divide up the fanbase. First it made it canon that the Uchiha were willing to kill fellow members of the village so long as their family attained power. Secondly it made it so Itachi's torturing Sasuke for years in order to "Give him strengh to rebuild the clan" was a sign of "love" instead of what it originally was suppose to be, the sign of a homicidal killer who enjoyed toying with his borther's mental state of mind.
Sasuke's "Revenge" theme ended with a popcorn fart instead of a final last stand. Today despite all his actions, he essentially works for the Leaf even if he isn't comfortable enough to be around them. That's right Sasuke Uchiha is now just the strongest warrior of the leaf villages arrisnal, and is "just super cool". Despite all the actions he tooked against the Leaf to begin with.
Sakura never surpasses Tsnuade in any measureable way in the end. Tsnuade is still working at the front of medical technology, and is still trying to improve her skills even though she is technically a retired Hokage and has every right to just sit around all day is she wanted to. Sakura on the other hand is living as single mother, is completely in debt, and destroyed her house because her daughter asked why their father abdnonded them.
Naruto became the very kind of person he originally hated. In the end he has little to do with his family, did nothing to change the system in any meaningful way, doesn't protect the weakest, and in the end is Hokage pretty much because he is the most popular. He also isn't above using underhanded tactics to get what he wants, including trying to sleep with Sakura simply because he thought it would upset Sasuke, and forcing Tsnuade to retire from being Hokage despite the obvious fact that she is still able to work.
I can go on. Like a mosquito on a nudist beach I really have a hard time deciding where to start and end becuase their is just so much out there to work with. I may come back to this later, but this is enough for now.
Persona 5 hype 
The Gold Saints
