I have to disagree with your statement that Naruto neglects him and deprives him of needed attention. Holding down a job to support your family and community instead of playing with your child 24/7 is not neglect. It is just being responsible and doing your duty as a parent (and as a leader if you are in a position such as hokage). Boruto acts like he is entitled to his father's undivided 24/7 attention, and that is a flaw of Boruto in my opinion.
Even while holding down the job, Naruto is still kind and considerate enough to at least leave shadow clones for Boruto. Yet Boruto doesn't even seem to appreciate that. I don't know why people look down on clones so much. Once the clone disperses, the real Naruto will still get all the information and the experience. Therefore it will be as if Naruto was really there.
The only thing that I think Naruto messed up on was Himawari's birthday party. He could have made some time in his schedule for that since a birthday only comes once a year (unlike the 24/7 play time that Boruto seems to want). At the very least, Naruto could have had his clone be in sage mode so that it was more durable and less likely to disperse.
Other than that, I don't think Boruto's attitude was ever really justified.
I wonder if Asuma ever hassled Hiruzen like Boruto did with Naruto.
A large reason why the shadow clones were looked down upon Boruto, was because Naruto himself wasn't consistent with them. Honestly I don't really think he had a problem with them that much, he often asked his father if he was the real one or the clone version, which I'm sure is very frustrating due to how many times he must send those.
I guess from his point of view, he could never really tell which one was his father, and which was one the clone. Just because it gets the same experience and knowledge, doesn't make the situation any better for both of them. What is known is that Naruto can't be there himself, and Boruto understands this.
What bothers him is the fact that he seems to think that Naruto neglects them all - Not just him. When it was his birthday, Naruto was absent, not a shadow clone present, he wanted to make sure Naruto was there for his Sister. Naruto was the first one to arrive after a bit of shopping, and, that really shocked him. However once the party started, soon enough the clone dropped the cake as it was being brought to the table, and then they all realized that Naruto had sent a shadow clone instead of being there himself. It's hard to question whether or not it's just the shadow clone being sent which angers him, or the fact that Naruto himself ruined the birthday for his sister because the clone exploded.
I'm assuming that Naruto comes home really late anyway, after work. So they don't really get to see each other or spend time during the day.
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When it comes to his anger/rebellious attitude being justified. I guess that goes down to where it actually happens. Outside of his lazy/not hard working attidude, the only real time we see him 'angry' at his father to the point where he's furious was the cake scene, and when Naruto disqualified him for being a shinobi, and said that we would 'talk later'.
To him, it's clear that he understand Naruto is incredibly busy that he can never truly make the time to see him, even if it is a shadow clone being present. That goes down to whether you think a clone is acceptable in his stead. Sure, sometimes it is, but the Movie showcased that it isn't always perfect.
If you go back to the scene when Naruto stands up after his clone parted. He said "Father... I messed up again"
Implying that something similar has happened. The cool thing is, you can't really blame Naruto that much on his fatherhood, because he never really had a father to begin with, plus, no one taught him how to be a father, and run the Village at the same time. It was a nice conflict in my opinion.