I guess it was the case when the author invested too much in his favourite character and was unwilling to modify the end goal for him, better ending for him would become the real villain and especially a personal to death nemezis of Naruto, would be great contrast with how Naruto personality was just straight up doing wololo to tons of people but failing for the one he considered his closest friend, that would also give some depth to Naruto’s personality.

Especially visible how the author generally have no trouble writing good characters, for example Itachi was actually very impressive not only for a manga and a real tragic character in the story. Even Naruto himself, while being the same annoying bubbly liberal type as is common in the animes, had a lot of quirks and traits to ease that up and ultimately ended up being pretty ok consistently (except his obsession with Sasuke, that would be great if he wasn’t ultimately forced to be correct by author).