Kishi messed up a lot of things. That whole manga had some serious potential. Should've kept the reincarnation shit out of it.
I don't see why a bunch of people hate the reincarnation stuff. That was all great in my opinion! The thing Kishi messed up on in my opinion was his consistency on plot points towards the end of the manga (mainly stuff regarding the Otsutsuki). For example, it had been earlier established that Hagoromo defeated the juubi and sealed it inside of himself, and then sealed its shell within the moon on his death bed while creating and scattering the bijuus. In fact, Hagoromo himself actually told Naruto that they sealed the juubi inside of himself. However, later the manga made it seem like Hagoromo and Hamura immediately sealed the juubi inside of the moon at the end of the battle. This of course left me and a bunch of other people wondering about the questions of: "When then, did Hagormo become the juubi's jinchuuriki if they immediately sealed it in the moon? Also, if they could have just immediately sealed it in the moon in the first place, then why even bother making Hagoromo a jinchuuriki at all?!"
The anime tried to rectify this situation with those Otsutsuki fillers, but SP just ended up creating more questions than answers. For example, SP tried to answer the first question above by depicting Hagoromo and Hamura as fighting both Kaguya and the juubi separately, yet simultaneously. In the end, they sealed Kaguya herself into the moon via rikudou chibaku tensei, and then Hagoromo absorbed the juubi and then split it into 9 souls. This leaves the question however of: "What about the gedou mazou? How did that get up to the moon then, if the brothers only sealed Kaguya herself and not the juubi? Wouldn't this require another rikudou chibaku tensei, which would make another moon, or did Hagoromo just somehow teleport the mazou to the moon's interior?" Also, the anime depicted Hagoromo dying of either old age or sickness in his bed. However, assuming that he did ultimately rid his body of the mazou and seal it into the moon, he should have died due to the loss of his bijuus and the mazou in a similar way to how Madara died at the end of the war.
Then of course there was that whole Indra with Sasuke's MS fiasco, which was kind of a slap in the face to Madara since Madara was also Indra's transmigrant, and his MS was different.
Other inconsistencies with that filler include the fact that "The Last" established that after the battle with the juubi, Hamura took control of the Otsutsuki clan and went up to the moon with them, but in the anime, Kaguya came to Earth alone, and Hagoromo/Hamura didn't even know about the Otsutsuki clan.
In short, Kishi's first big error was consistency.
The other big error in my opinion was his lack of explaining certain powers towards the end (and by certain powers I mainly mean RSM). The databook gave a very loose explanation of it, but that clearly wasn't enough, as fans still dwelled in confusion over the form for years (probably even to this day). In my opinion, all of the conflict over RSM could have been avoided if he didn't mess with the design of adult Naruto's mode(s) and just had him go into the exact same RSM mode that we saw in the battles against Madara, Kaguya and Sasuke (with 9 tomoe and rinnegan symbol on the back, truth seeking balls and all).
He shouldn't have nerfed Naruto to begin with, but because he did, we now have to deal with a very BSM-like "Kurama chakara only RSM" which causes some people like Sensei-Sama to say stuff like "Naruto lost RSM", or "Adult Naruto still has RSM, but he hasn't used it" or "Naruto lost the bijuu chakaras, but he can get more via ninshuu or via being the meeting place".
That is one way in which I sometimes wish Naruto's modes were like Sasuke's doujutsus. At least there is no debating whether or not Sasuke still has rinnegan because it is a shiny purple obvious eye! We don't have to deal with all that "He lost it" "No he still has it" crap with Sasuke.