Shonen anime, especially ones focused on battling, tend to have very stereotypical main characters. Most of them follow the same general "blueprint" of being airheaded, good-natured, unimaginably stubborn in their ideals, and overall exceptionally hard workers.
But, as the genre has evolved and authors have experimented more and more with their storytelling, this isn't necessarily true anymore. And, even in the stories where there still are stereotypical MCs, they often go through massive character development throughout the course of the story that leaves them wildly different from the person they once were. To prove this point, let's take a look at some of the protagonists who change the most throughout their adventure.
8 Gon Freecss: Hunter X Hunter
Gon Freecss has to be first on this list otherwise Hunter X Hunter fans would blow a fuse. Now at first, Gon seems to follow the standard formula since he's naturally gifted, likes to help those around him, seeks adventure, and is absurdly stubborn. But, as the story goes on, it becomes increasingly clear that these aren't exactly the traits people thought they were and Gon is actually a much more dangerous individual than he first let on. By around the time of the Yorknew City arc, readers and viewers of HxH have noticed how exceedingly selfish rather than stubborn, willingly ignorant rather than cautious, and morally grey rather than good-natured Gon is.
And, once they get through Greed Island and into the Chimera Ant arc, this slippery slope Gon is on only gets more and more slippery. By the end of the arc, Gon is so full of hatred, anger, self-loathing, and overall malice that he gives up everything just to get a chance at paying back Neferpitou for everything she did to Kite. This sequence and the subsequent one-sided battle are truly haunting, especially since this sort of tone is saved for Killua, and are something that no one would have ever expected back on Whale Island which is exactly why HxH is so top-tier.
7 Monkey D. Luffy: One Piece
Now, this next choice should make a lot of sense, given the amount of time, episodes, and chapters One Piece has had for its characters to change naturally over time. And, while a lot of what makes Luffy, well, Luffy is exactly the same, he's by no means the same person or pirate he was back when he first left Dawn Island.
In all respects, Luffy has changed and matured. He doesn't think about what would just be the most "fun" anymore, he now considers his crew and the people around him constantly, and he's taking an active role in stopping the forces that he feels should not be in power. Not only that, but Luffy has visually changed a ton as well, with his chest scar and Gear 4/5 forms being the most obvious examples.
6 Yuji Itadori: Jujutsu Kaisen
Jujutsu Kaisen is an example of a battle shonen series that has quite the absurd breakneck pace. There's never a dull moment in this story as Yuji Itadori is constantly facing strife, whether its from curses all around him aiming for Sukuna's fingers, Sukuna himself, or just the other Jujutsu Sorcerers wanting to get rid of both Sukuna and his vessel.
And originally, it seemed like Yuji was able to take all this strife in stride and come out the other side a more positive person. But, over the course of Jujutsu Kaisen's events (especially during the Sibuya Incident arc), Yuji changes quite a bit. Eventually, he sort of accepts that no matter what he does, Sukuna is always there right around the corner with his awful smile to counteract his good deeds. Because of this, Yuji in the manga is much less chipper, has almost no self-worth, and just wants to do whatever good he can while the option is still there.
5 Ken Kaneki: Tokyo Ghoul
Out of every character on her, Ken Kaneki is the one who has the most obvious change throughout the story. Originally, Ken was just a quiet bookworm with few friends and a lot of repressed emotions. But, throughout the story of Tokyo Ghoul, Ken Kaneki goes through a real metamorphosis and comes out the other side something entirely new.
Not only does Kaneki literally change from a human to a half-Ghoul, but he also becomes a lot more violent, dour, and seemingly mature of necessity to survive around the other Ghouls. And to top it all off, he also literally loses himself and becomes an entirely different person during most of Tokyo Ghoul Re. Haise Sasaki is Ken's name throughout a lot of Tokyo Ghoul Re's events, as Ken has lost most of his memories before this point. And, when (and if) he does ever wake up, Ken becomes something even more than what he was before.
4 Eren Yeager: Attack On Titan
Eren Yeager, the main character of Attack on Titan, is one of the best examples of a protagonist who goes through a massive change. But, compared to a lot of other characters here his change is much less gradual and much more sudden. Of course, his change from the angry and vengeful recruit to the more mature and determined veteran Scout was gradual. But his descent into eventually becoming a "villain" felt a lot more like he made a decision internally, steeled his resolve, and had a massive sudden shift in personality.
By the end of Attack on Titan, there are bits of the original Eren that still shine through, but for the most part, Eren Yeager goes from a standard (albeit angry) shonen protagonist to a truly dangerous and broken man who made the only decision he felt he could.
3 Thorfinn: Vinland Saga
To be frank, the gradual change of Vinland Saga's protagonist AKA Thorfinn is sort of the entire point of the story. It may not seem that way to anime-only viewers of season 1, but manga readers are exceedingly aware of this fact.
So, it goes without saying that Thorfinn is one of the protagonists that change the most because his character arc is the crux of the story. All that said, it still needs to be said that Thorfinn's gradual change is so exceptionally well-written, believable, and understandable that it's one of the primary reasons this story stands among some of the other all-time seinen greats like Berserk and Vagabond (even if it's a bit more battle shonen than it is seinen).
2 Shigeo Kageyama: Mob Psycho 100
Compared to a lot of other protagonists on here, Shigeo AKA "Mob" might not have the most drastic or immediately obvious change in his character over the course of Mob Psycho 100's story. But, the lessons he's learned through all of his encounters, battles, major life events, and the ways he's suffered along the way have absolutely changed how Kageyama thinks, acts, and approaches life.
In fact, the entire focus of the first arc in season 3 is based around Kageyama thinking he's popular and getting a bit of a swollen ego because of that, which would have never happened at any point before this.
1 Naruto Uzumaki: Naruto Franchise
And lastly, this list just wouldn't be complete without including the seventh Hokage of the Hidden Leaf, Naruto Uzumaki. Naruto originally starts his epic as one of the more irritating and misbegotten characters in the cast as he tends to alienate those around him, is constantly causing trouble for attention, and is tirelessly posing or spouting the same couple of lines about "believing it" and his "ninja way".
But, throughout the course of the original Naruto series, Shippuden, all the movies, and eventually Boruto, this Nine-Tailed Jinchuriki goes through a lot of character development. Granted, it's a lot more gradual and isn't nearly as immediately obvious compared to many other shonen protagonists. But, the version of Naruto who runs the Hidden Leaf in the Boruto series is undoubtedly a completely different person compared to the kid defacing the mountain of past Hokages.