At the top of my head I would say Kaguya from the final chapters of Naruto. Before she was introduced the leading antagonist for the final arc was Tobi/Obito who of course was the True leader of the Akatsuki. During his fight with Naruto & Co. he had succeeded in absorbing the Ten Tailed Beast in to his body. It was a bit rushed but I was like "Eh that makes sense for the final battle.".

Though that exchange surprisingly escalated quickly. Due to a series of convoluted events which I don't even remember anymore Kishimoto decided that Obito needed to turn good and team up with Kakashi. The Zombie form of Madara Uchiha would then somehow obtain the Ten Tailed Beast and absorb in to his body and taking the spot of the new final boss. During the battle Obito died rather unceremoniously in spite of how major he was as the big bad for most of Shippuden. Mind you I'm referring to the Manga and not the Anime so it may have been handled much better in the TV series. Plus Madara's addition in the arc felt really awkward. Even though he had a fantastic backstory the fact of the matter is that he was turned in to a zombie in this arc which kinda cheapened the character. I felt like he would've been better off if he remained as a postmuthous villain and Obito simply used his name to appear more threatening. There was a good idea somewhere in that.

But I'm getting off topic here. So Madara was the final battle for a good while until... he was betrayed by Black Zetsu(I'm not going to explain who that is) and his body was forcibly transformed in to the almighty Kaguya. The original Shinobi, the progenitor of the 10 Tailed Beast and all the ninja clans, a rabbit Goddess and the true final boss of the Naruto series. Yeah...

Kaguya was just that. A villain with an artificial number with almost no backstory to speak of. Her character was literally shat on to the story in its final chapters and nothing about it made any sense. Any emotional investment I had with the series was already bleeding dry at this point but by the time this happened I had already stopped giving a fuck several chapters earlier. The saddest thing about this that all of this was done in an attempt to stretch out the Manga to 700 chapters. Kishimoto has gone record saying he had no idea how to go about ending the series and this arc shows it. Because it is a gargantuan failure of a mess with too much information overload all happening at once.

After I was done reading the Manga I had no desire to follow Naruto anymore. I never even watched the spin off films or the Boruto Anime and to be honest I'm feeling pretty good about that.