Honestly, the biggest thing for me was poor pacing in the last arc and drawn out end villains, minus Kaguya of course. The time and effort Kishi put into Obtio was heinous and the time Madara spent toying with his opponents as an Edo and alive with no eyes was just a waste of time.
Kishi wanted to hold back Obito's identity for as long as possible and that became painfully obvious toward the end. Obito had such a strong will to survive as long as he did, but yet he was so easily manipulated and corrupted by Madara? His whole story lacks logic and is quite disappointing. Granted, Tobi being anyone else would have been just as illogical, but Kishi literally made it impossible for Tobi to be anyone until he revealed Obito's screwed up past. The whole thing was a trainwreck.
As for Madara.... we get like 2 chapters of him at full power, 2-eyed, Juubi-jin epicness. This is after over a hundred chapters of edo Madara and no eyed-Madara. It was a real travesty considering the build-up the villain got. I could take or leave Kaguya taking his place, but either way Madara needed more Juubi-Jin screen time and less Edo/ no eye screen time.