We're all focusing on the love angle of the finale. But really, it's the disrespect of the themes Kishi set up in part 1 that bother me the most about this manga.
specifically, I rewatched the Neji and Naruto fight. Neji goes on about caged birds and destiny, but one thing stood out to me: Neji says something like "you aren't destined to be Hokage. You're a scrub." And of course Naruto defies this and punches some sense into Neji, changing his entire world view in the process. That's supposed to be the big takeaway here: that Naruto controls his own fate and passes that sensibility on to Neji, who is destiny personified at this point. Naruto brings up how he overcame his failings through sheer hard work, and that's the moral of his character
But then Naruto is actually the child of destiny. That entirely subverts his whole character. How do you even do that as a writer?
Here's how I would've done it. Make Naruto much stronger on the onset, as in stronger than Kakashi onward to Jiraiyas level. By this time, he should have already been ready to face off the average Akatsuki member. Condense part of Sage training, element training, and KB training into that three-year timeskip and PART of complete mastery of Kyubi. Kishi likes flashbacks, so when he displays his new technique that he learned with Jiraiya, just do a brief flashback on the key fundamentals that led to his mastery of them. That jutsu being specifically Bijuudama FRS that Naruto is warned not to use.
At the early parts of Part II, have what is currently his chakra mode be heavily implied but not outright. If I were to elaborate, if anyone is familiar with Dragon Ball, in some movies, Goku had what was a False SSJ transformation, most notably in the Lord Slug movie. Well, Naruto could have something similar to this, a False Chakra Mode, something like what he displayed against Gaara. It would be unlike the tailed forms or KNO. Kyubis chakra would take on the golden Yang properties and give Naruto an enormous but brief boost, and only attained during the most extreme of emotional duress and/or tedious concentration.THEN if it used too long, goes into the more unstable and volatile tailed forms. On that note, keeping Narutos confrontation with Orochimaru on the bridge as realization of how destructive he can be if he loses control kept in place. Although minor difference being Id have Orochimaru instilled with far more fear over this power, and serious second-guessing on whether he should have taken Naruto as a host body instead.
All of Narutos training then can be exclusively focused on mastering the two essential forms of Full Sage and Chakra Modes. The mastery of one being essential to mastery of the other. More specifically, having to master Chakra Mode BEFORE Sage Mode. The things like meeting his mom, reconciling with Kurama and all kept intact, but moved up before meeting his father. In the midst of it all, most importantly display Naruto learning and appreciating the responsibilities of authority and leadership. Promoting him to Jonin and mentoring young ninja, namely Konohamaru; having him take the lead on his own teams missions as well. To show that practically speaking he was growing to a Hokages role.
Last but not least,
completely rid of the concept of Child of Destiny. Narutos character definitely did not need that. If you must have it then have nagato have been the indisputable Child of Destiny, and having Naruto beat him and turn the fate of the world around be that much more profound. Showing that along the lines of what he said in Part I, would screw destiny if thats what he had to do.