Maybe the ANBU who raise Naruto are actually part of a secret group within the ANBU that has its own agenda. They could be training Naruto to be a weapon against a hidden threat in the shinobi world. As a result, Naruto's journey would be about uncovering this conspiracy while also dealing with the fact that his upbringing has made him an outcast among the regular shinobi. For example, he might be too brutal in his fighting style for the more traditional ninja.
Another plot twist could be that Naruto's ANBU upbringing gives him a different view of the Hokage. Instead of seeing it as a symbol of hope and leadership like in the original, he sees it as a position of power that can be misused. This could lead to a conflict within Naruto as he starts to question the whole shinobi system, especially when he discovers the secrets and corruption that the ANBU might be hiding. His journey then becomes about reforming the system rather than just becoming Hokage.