Easy ways to fix Naruto's hypocrisy:
#1. DON'T make him the 4th Hokage's son. A popular idea at the time we were all speculating, but a terrible idea in hindsight. If Naruto is gonna rise to the top through hard work, no notions about his lineage should ever come into the picture. The 4th could've given him the kyuubi as a means of saving a newly orphaned baby who was on the verge of dying as a result of getting caught in the crossfire during the kyuubi's attack. Not only would this solution fix Naruto's hypocrisy, but it would lend credence to why the village hated him and why no ninja has ever stopped to say "Hey, aren't you the 4th Hokage's son?" In a fixed version of the story, Naruto's parents are nobodies who died during the kyuubi's attack.
2. Give a better answer for why he has huge chakra reserves. None of this stuff about Uzumakis just having lots of chakra. Instead, Naruto naturally grew such big reserves over time as a result of having to suppress the kyuubi every day. Through his hard work, he became strong. Simple concept.
3. DON'T give him Sage of Six Paths Mode. His one and only powerup should have been sage mode. Make him win fights through clever use of ninjutsu (which should always be possible thanks to the unlimited number of uses shadowclones should provide) and his sheer unpredictability as a knuckle head ninja.
4. None of this crap about only loving Sakura due to his rivalry with Sasuke.
Love your ideas.
#1. I always felt like they gave away Naruto's THREE secrets too easily. First that Minato was his father. Second, that Kushina was his mother. Third, that he had the kyuubi sealed into him. All three were obscured, yet somehow everyone knows about it, and they treat Naruto like trash anyway. None of this ever made sense to me. Naruto should have been just another war orphan like Sai. A nobody. Not because of a huuuge secret though, but because only a few people knew Minato and Kushina had a thing. And then only a few other people knew Kushina was pregnant. And then, only a very few other people knew about the kyuubi and Minato's ability to seal it into someone. (Those people would be Jiraiya, Tsunade, Kakashi and probably Danzo and the elders. Anyone else who knew (like Itachi) would have had to discover it through nefarious means.) Then Naruto's birth, seal, and subsequent abandonment by the village becomes much less of a plot hole.
#2. Chakra reserves - Uzumaki backstory is so desperately needed here. I wish there was a Mina/Kushi gaiden. could have been explained there!
#3 - Yes, yes, yes - you're exactly right. His skills should totally support his knuckle-head ninja standing!
#4 - yes - that was a bunch of crap.
4. Only existed due to the last. 3. Completely agree with if they wanted to just be a cycle of conflict its fine, but once they made it an "actual" reincarnation conflict; the story went off the rails.
The problem with 1. Is that it really isn't explored then that it exist. Did all the adults even know that Naruto was the 4th's son, or did that even matter to them because as far as they were concern he could turn fox at any minute? All the questions of how Naruto was raised when he was young?
2. Could also be solved by exploring the Uzumaki clan instead of just focusing on the uchiha's for the entirety of part two.
Yes, exactly. The immense chakra reserves thing is RIGHT THERE in the story: in Nagato, in Karin and in Kushina. All they had to do was develop it just a tiny bit to justify Naruto's giant reserves. After all the time spent on the Uchihas back story, it would have been so simple to have developed the Uzumaki line just a little bit. But nope.
In regards to #1, if the author is going to make the point that anybody can rise to the top through hard work and that Neji is wrong about having to be born into the right family and whatnot, Naruto needs to come from nothing and the author needs to avoid ever making Naruto's lineage an issue. As to how Kishi could have gone about doing this: After a long and gruesome battle against the kyuubi, the 4th is just about dead. He sees a dying baby over yonder, realizes that its parents are dead and that its dying as a result of the collateral damage from his fight with the kyuubi. Seeing no other options, realizing that the kyuubi needs to be sealed and making one final act as the Hokage, he transfers the kyuubi into the baby.
Yes - that could totally work. Naruto is literally a war orphan with some exceptional properties. That would work out great. I have a rough outline for a fix where Danzo raises Naruto (like Sai), and Naruto's parentage is not a part of the story. Doesn't need to be. So yeah, that solves that whole problem. The reasons why they hid the facts of Naruto's birth parents/situation, from himself and the village, becomes a much bigger problem for the plot because Kishimoto did not go back and develop it.
In my other big fic, A Voice in the Wind, I tackle this as well. In my story, Konoha decides to completely hide Naruto's name, identity even existence. The fact that he was the jinchuriki was only known by one or two people. And most of the village had no idea what it even meant. Only elite nins from hidden villages or most prestigious clans knew what a jinchuriki was or how it was contained. So instead, Konoha broadcast someone else as their 'chosen one'...Sasuke.
There is so much in Naruto that is lacking: backstories of Minato and Kushina and their clans; the jinchurikis and their backgrounds; the bijuu and how they came to be. So much of the focus is on Sasuke and the Uchihas, unfortunately. So it's left to the realm of fanfic to explore all that.