It is a pretty big problem with Shonen of the 20th Century, though I'd say Luffy from One Piece and Toriko from...Toriko are bigger examples of such than Gon, though the uniqueness of Gon's character indeed only becomes apparent slightly in the Yorknew Arc and fully in the Chimera Ant Arc. There's also Naruto taking a lot of traits from Goku, though most of them are purely stylistic and visual similarities are far from the main problem with his character.
As SHC mentioned, there are a few post-80s protagonists in Battle Shonen that don't suffer from being Goku clones; Himura Kenshin from Rurouni Kenshin, Higashikata Josuke, Giorno Giovanna and Jolyne Cujoh from Parts 4, 5 and 6 respectively of JoJo's Bizarre Adventure, Urameshi Yusuke from Yu Yu Hakusho and Edward Elric from Fullmetal Alchemist being some of the main examples.
It's not as though Goku clones has been the first main fad for Shonen. Back when Hokuto no Ken was Jump's cash cow before Dragon Ball took its place, everyone was creating Kenshiro clones that had even more blatant similarities than the Goku clones such as Tsurugi Momotaro from Sakigake! Otokojuku being delinquent swordsman Kenshiro, Saeba Ryo from City Hunter being pervy gunslinger Kenshiro, or Jonathan Joestar from JoJo Part 1 being Victorian gentleman Kenshiro. These were even more shallow knockoffs than the post-80s Goku clones as aside from aesthetic differences, they were all just shallow representations of Kenshiro's character appeal (with the slight exception of Jonathan at least having some unique character traits).
That said, many Shonen protagonists in the modern era, even if not based on Goku or Kenshiro, still end up being watered down versions of better protagonists, Edward Elric and Jolyne Cujoh being the only real exceptions from the 21st Century. Ichigo from Bleach is as bland a protagonist as you can get with traits clearly taken from YYH's Yusuke and Seiya from Saint Seiya, Gintoki from Gintama took one too many inspirations from Kenshin with his comedic nature being the only strong difference and the less said about MHA's Deku or Black Clover's Asta, the better.
That said, it's best to avoid the mainstream when it comes to a lot of Shonen and look at older titles if wanting more originality in a Shonen protagonist, Yabuki Joe from Ashita no Joe being a shining example of one that breaks the demographic's mould.
