Can't say I like any character in the manga bar Sasuke and Sasori. Danzo was decently written when they reduced him to a caricatural villain somewhere halfway. I mean, he even has the "muahahah evil-eye-patch" thing going on. Orochimaru was pretty decent in part one.
For me, personally, any badly written, unrealistic character should have been restricted in the plot. Kakashi and Bee should have died; Kakashi against Pein and Bee against Sasuke. That would have impacted the story in multiple ways. Pein brining everyone back to life robbed Konoha of the comeuppance it rightfully deserved. Setting up various Deux Ex Machina to hinder Sasuke's progress to take down Konoha was another terrible side to the plot.
Anyhow, these are the flat, terrible characters that should have been cut off or restricted in the plot ages ago:
- Kakashi.
- Bee.
- Naruto - the guy that carries the name of the manga is a shining example of how to write "Gary Stus." Kakashi is not far behind.
- Hinata.
- Sakura.
- Hashirama.
- Obito - the final arc for this guy was painful to read. Too painful.
- Tobirama - he was squandered potential. The things Kishimoto could have done with his character to delve deep into the age long conflict. But, instead, he reduced him to a man with a foolish, single-minded agenda that clashes with his genius jarringly.
- Ae - what's the purpose of this guy, again?
- Shikamaru - he is lazy and he's a genius. Full stop. Why was this character never cut off? Some one needs to remind me of this.
And many ... many more.