Kaguya was listening to her own creation to tell her what to do. She did not have her reasons explained. She was the one that started all, yet appeared a few chapters before the manga ended. She was mentioned for the first time when the Manga very late and her story contradicts what was previously established.
Hagoromo was mentioned and hyped as the creator of Ninjutsu and the strongest person to ever exist, defeated the Juubi by himself and created the moon on his deathbed. None of that was actually true. On top of that, his looks and powers are different from what he was hyped to be like. On top of that he had a brother who helped him fight Kaguya. And that brother had no real purpose in the story other than explaining Hyuuga clan's history.
Madara was very well developed but his death ruined his role in the story.
Obito was well developed but the whole idea of him being Tobi is questionable, as well as Rin being shown as reason for some of his decisions.
Tobirama was very well developed but he hasn't been shown using water Jutsu he is so proud of. I understand that he couldn't use them against Obito. But his fight with Madara should have been longer and more epic with many different Jutsu.
Minato was very well developed. But after he was revived many things about him were revealed that made him look somewhat childish and quite inexperienced.
Naruto is the most developed character in the story but the way he received his power from Hagoromo was very lame. And the fact he let Guy live was very disappointing. On top of that, the way he dealt with Sasuke and other characters was not the most well done. And after he became Hokage he is not as impressive as he used to be.
Sasuke changes his ambitions too frequently. At one point he wants to kill everyone, then he suddenly has a different intentions.