I don't want anyone to bite my head off. So I'll just go ahead and say I think these are all a personal taste thing.
I don't necessarily consider them bad but maybe flawed. At least to ME personally. So basically I'm not being objective about most of these. And my reasons may not even be good so I'll acknowledge that for you here and now. It's all just personal. There's something that's stopping me from enjoying them entirely.
For me it's the Air Gear manga. I'm sure someone will get angry at me for naming that but near the point where Kururu shows up I just felt like...I was reading something different entirely and I just couldn't get into it as much anymore. I always say it turned into some weird Final Fantasy (On roller skates) thing. I dunno if that's even a good comparison but like it just stopped feeling like gang wars and turned into something ridiculous. Like maybe it's just my personal tastes but I just didn't like that the scale got as big as it did. I felt myself eyerolling. I'm still able to sorta enjoy character interaction stuff but do I actually enjoy reading it at that point? Not really.
I also wanna say the Shaman King manga. Which is ironic because when I was 13 up to like age 17 or something it was everything to me. But then there was a point where I just felt like the spark to it died. I think it was somewhere near after the golem arc? I'm not exactly sure why I started to feel disconnected. I don't know if it was just me losing interest naturally or if it was the manga itself. I know I'm capable of liking a series for a long time like with Yu-Gi-Oh which I started when I was like 8 and I still like it. So Shaman king just...started doing something and I just couldn't anymore with it.
Pupa (Manga). This might be easier to explain. It's just flat out bad. The creator might be new to making manga or something. And it's not bad because I dislike gore and subtle suspicions of incest because those are two of the reasons I manage to like the series at all. It's got sorta blandish characters though I do like Utsutsu a lot. But the plot is just..eh. I dunno if people are as caught up as I once was since I got in pretty far via japanese scans. It doesn't really get better. I guess I like it because it's a bit simple and I sorta like the characters. The anime actually managed to make it even worse so I don't even like the anime at all.
One Piece. (P-please go easy on me) I feel scared to say anything about it because it's fanbase is pretty hardcore. But. I'll just say why I personally have trouble with it. Firstly, it's ironic because two of my favorite characters of all time are in it. (Shanks and Ace. Actually Shanks IS my favorite character of all time) But I just feel like as it drags on and on and on I've lost interest. New arcs appear, new characters, and usually I barely care. I'll skim through but as hard as I try I just can't seem to stay interested. And I can't seem to develop any bond to the straw hats. Like I'm cool with them but with other series I gravitate easier to characters and with this I feel stand offish towards them. With that said, I do think the artist is really creative and I really really love some of the side characters.
Mirai Nikki. I love the idea behind it. I'm a big fan of battle royales and violence. But I loathed Yuno and Yuki so much and rarely enjoyed them as characters. I only could enjoy the situations surrounding them. And since they're such a huge part of the series, it was a real downer for me.
Blood Lad. I really like this series but one of the biggest parts of the story as well as one of my biggest issues is that it's main sub plot is basically a horrifyingly boring love story between Staz and Fuyumi. Fuyumi is literally a useless moe girl who exists to be a love interest. If I can't like the girl how could I possibly be interested in any romance with her, especially when that's one of the main plot points.
Highschool Of The Dead. I do like this series because of zombies and action. But sometimes if characters feel too overpowered I lose interest. Also I despise Rei and she's a huge character so yeah.
Inuyasha. I felt the dragging of Kagome and Inuyasha's relationship to be very irritating and got in the way of the good stuff. Prob a dumb reason because it prob sounds like typical Kagome bashing but..
Naruto. I got over my "lol ew Naruto" phase a while ago and don't mind admitting I like it. (Mostly just cuz I like all the side characters) But at the point where Sasuke joins the Akatsuki and plans to take down the leaf I just felt like the series was getting a little eh. But I could still tolerate it. But then this recent arc of the final war. I just...can't even take it seriously even remotely. Sasuke suddenly changes his mind and all that buildup that Sasuke would be an ultimate enemy goes straight out the toliet. The whole thing with Kabuto bored me but wow even that was almost more interesting than Tobi + Madara...and then Tobi backing out as a villain...and then Madara doing what the hell ever and now there's some...girl bad guy? I don't even understand. The fact that the original Akatsuki and Pein was more effective and meainful than this supposed end to the series is disappointing. The finale is just being dragged out at this point and too much is happening all at once and I just think this is hurting it. Also they should just rename the series to Infinite Eye Pupil Designs: A Ninja Story.