Kishi made a few mistakes, but nobody is perfect. To write a manga for 10+ years and continuesly come up with new ideas and ways to conclude it is no easy task. I respect kishi for his work, and naruto will without a doubt be remembered as one of the greatest mangas of its time. With that being said, things could have been done a bit different.
If I were to ever produce a manga, I would start with the ending and work my way towards the middle, before starting from the beginning. This solves a few problems with inconsistencies. I would also make sure I have my final antagonist in mind from the start to ensure that some hints/references could be made later on.
I don't think kishi did this with some aspecfs of Naruto. There were some definitive inconsistencies throughout the manga. Obito was not a well thought out character, his reveal really broke the pace the manga was following up to that point, and everything felt forced after that. The juubi was rushed, and taken away/dealt with too fast and too easily. The "progenator" of the naruto universe being a gigantic chakra monster with sinister emotion, should not have been controlled so easily.
Madaras defeat was rushed, I wanted to see what he was capable of with double rinnegan and the third juubi sharingan. Being stabbed in the back by black zetsu was completely ridiculous, and in no way should have brought him down.
This brings me to Kaguya. In my opinion Kishis greatest mistake. Kaguya had "potential" as a final antagonist. I say this because, if she had been mentioned earlier on in the manga, it would have made her coming back all that more terrifying. For such a "god" like character, she lacked any real strength or intelligence that made her anymore divine or deserving of that title. Her character was never really fully explained, nor were her actions or reasons for bringing about the infinite tsukynomi. Why did she exist to be a final villain? What was her purpose? Her story? Why should she have been feared more than Masada or obito? You see there was nothing that made her special or unique.
She lacked character development, and a reason for "being" black zetsu was wasted as intelligence, and did nothing but order around this "god". Had she been revived earlier, or talked about more. Given the opportunity to understand her character, or her true motives might have put her in the deserving spot of "final antagonist". I wanted someone who pushed the boundaries of the alliance. Deaths, depair, torture or sadness! Something that made the characters doubt the possibility of handling such a "god" but instead she was sucker punched by a naked clone.
End of rant. Sorry for the wall.