The Naruto series is filled with plot holes and it is not even funny. So much revisionist history takes place that completely undermine the whole plot of the series.
Sarutobi being regarded as the strongest in P1. More of a retcon than a plothole, but eh.
The blatant ignorance regarding the Uzumaki emblem. I do feel like people would treat Naruto a bit better considering there was only one Uzumaki left in the village, and said symbol is displayed even on basic jonin vests.
Minato's kurama link mode; unless he somehow bonded with Kurama whilst mindlessly fighting the other kages (unlikely? we don't know!) and ended up with some semblance of control over its chakra, we don't even know if his form would turn out the same as Naruto's or more basic like Bee's. Too much at play, and this could delve into many things like how the hell Naruto's form was so different, or just what is the reaper death seal (though both of those could probably be theorized in an essay I'm too tired to write.)
An extra is how Naruto didn't get immediately kidnapped, unless he wasn't able to Kamui into the barrier or something. I've wrote something of a story about this.
