1. Sakura -- Got shit on the whole series. Even Kishi admits it was hard to find ways to include her. That's not a good sign for a "main heroine." He really needed to give her a backstory, make it relevant to the overall plot, and give her multiple arcs. People can't even imagine that, with her current implementation, and he wrote himself into a corner where fans wouldn't tolerate "Sakura-heavy" chapters, so eventually he was stuck with basically "Yeah, sorry, she's in this chapter, but look, there's also a Susano'o!"
2. Orochimaru -- This villain never got a proper arc; he was sort of a red herring. He was always "defeated" in unsatisfactory ways after the Akatsuki had completely overshadowed him as a threat/villain. However, later on, I liked the "not quite a villain anymore" Orochimaru, although his character development needed to be explained more. I think being humbled by Sasuke/Itachi, combined with witnessing Kabuto's failed attempt to live out Oro's philosophy, and finally learning about Jiraiya's death, all made Orochimaru question the value of his previous goals.
3. Madara; he was one of the best-developed villains in the series (either tied or second to Obito). He was a far better final villain than BZ/Kaguya, and inexplicably got backstabbed, despite having Sage Mode sensory powers. Guy's Evening Elephant couldn't punch through his back, but BZ's finger-jab went straight through his heart. That's plot.
4. Kabuto; he just got rekt by Izanami, the ultimate "Mind **** no Jutsu," and came back an entirely different person.
5. Killer Bee; he was a major player in the War Arc and the battle against Obito until the Shinobi Alliance showed up, and then he was suddenly basically written out of the series. Kishi really had to come up with lame ways for him to "contribute" while not stealing any of Naruto's thunder. Probably should have just given Bee an epic death.
6. Kaguya; defeated by a single "tag" from Naruto and Sasuke. Not really "trolled," but it's a lame way to go. She's obviously invincible, otherwise. Only other way to stop her is to somehow steal her chakra.
7. Nagato; not only was he a pawn (of a pawn of a pawn of a pawn), but his whole ideology was refuted by a very brief encounter with Naruto, who used some very vague logic and TnJ. Naruto did a much more convincing TnJ against Obito, and the TnJ in that case was built up over many chapters of interaction and explanation. Against Nagato, it was far less well-written, and felt somewhat unsatisfying. It was obviously meant more to develop Naruto's character and set things up for the War Arc and the conflict with Sasuke; Nagato himself was written off as a plot device at that point.
8. Suigetsu; really has no reason to exist after Sasuke joins up with Tobi. Suigetsu never got the swords, and in any case we never will get to see him use them. His character/goal were just forgotten. I think Kishi intended to do more with Taka; they should have been involved more in the early War Arc (Sasuke's absence was too long). Suigetsu should have somehow been there when the Seven Swordsmen fight happened. In fact, that entire fight needed to be extended, rather than being off-panel. I'd rather have seen that, and skipped the abomination that was the Kin Gin bros.
9. Hanzo was also trolled. Obviously it's impossible to see him defeating the Sannin with that level of skill. They were either weak as hell at that point, or Hanzo was trolled. There's no way Mifune is actually too fast for Hanzo to use any jutsu.
10. Edo Minato; never used that big jutsu he kept hyping, and eventually had to spend several chapters fighting without any arms. Like, why the hell did Kishi need to take Minato's arms?! He was already a balanced character; he couldn't really contribute that much to the fight outside of Bijuu Mode, and was better off giving that chakra to BSM Naruto.
11. The Bjuu; they're a bunch of badass chakra monsters. They were freed from Obito, only to be caught by Madara within a few chapters.. and then freed from Kaguya, only to immediately be placed under Sasuke's Genjutsu. Really sad day to be a Bijuu.
