I haven't seen Naruto mentioned yet, the entire show is redundant and eventually contradicts every theme it tries to establish but it's plot holes kill me.
The Akatsuki serve no purpose, there's no reason to assemble this group of bad guys and wait 3 years for Naruto to come of age when Black Zetsu has been manipulating events for hundreds of years and has what he needs to revive Kaguya with Obitos Rinnegan and strength alone.
Obito's actions make no sense he has no motivation to attack the leaf, and once he learns of the rinne rebirth jutsu why wouldn't he revive Rin.
Retcons constantly: Naruto channeling the fox Chakra on command as a kid only to lose that ability, Hiruzen promising to raise Naruto then abandons him, Shukaku being a priest until they decided they liked tailed beasts and he was the 1 tail.