One of the things that just feels wrong about the ending is how it pushes conformity. Sure, traditional Japanese values. But shonen is meant to be an escape from that, with it's protagonists following their dreams, defying authority, and fixing broken systems. It's rooted in the Japanese generational gap. The older people want the younger to follow them obediently, while the younger generations have seen the failings of the older ways.
With Naruto, it's about enduring suffering to continue those systems, submitting to tradition, and turning having Naruto achieving his dreams turned into a joke. It's taking the side of the adults, especially in Boruto, and then the people making it wonder why it isn't as popular as Naruto was back when it was emblematic of what shonen is meant to be.
Exactly. Look at other shonen series.
Yu Yu Hakusho ended with Yusuke travelling to the Demon World, and when he got there, instead of allowing the realm to fall into war, he set up a kind of "violent democracy" for the demons. In addition, he and Koenma had discovered Enma had secretly been allowing powerful demons to slip through the barrier to justify it's existence (today, this sounds ERRILY familiar)
Rurouni Kenshin was very critical of the Meji government, and while it did not advocate for outright rebellion, it did emphasize the shades of gray a government can have and how the next generation has to change the world (the right way).
With current shonen, Bleach had an entire arc about Ichigo and friends going against Soul Society, just to save one person. One Piece is about Pirates, so...yeah. Fullmetal Alchemist also showed the brothers going up against a conspiracy millennia in the making within their own government.
Heck, you can look at what's going on with Shokugeki no Soma right now. I guess this one's more complicated, since Azami's plan is "technically" the revolution, but it's one that's eliminating individual freedom and thought. Despite how cutthroat the original Tootsuki could be, Soma and friends loved that they were able to challenge and express themselves. So Azami's revolution is arguably quite Japanese.
Though it is Seinen, Akame ga Kill also dealt with corrupt governments, though the antagonists are so evil that realistically they wouldn't last long without erupting into civil war.