Many, but here is my favourite punchin bag Sword Art Online.
Bad written characters are imo always fatal flaws for a show and the reason why i end up disliking them, why should i care for characters who have a plain flat personality and also having a mary sue character as protagonist (a mary sue character doesn't have to be bad, but in most cases he/she is) and not to forget that in the several months this show takes place no character evolved in any kind the only character that changed was Asuna she devolved from being kinda cool to being just a useless pile of crap for the sake of making the mc rescue her all the time.
The setting would be kinda nice but the author failed to make the world believeable or actually working (if this was an actual mmo it would be to broken to be launched after the trainwreck of the beta it would have been).
Bad Pacing. lets make the story several months long but skip a lot of it because why the shit not...
Plot holes, a game and gamingsystem that shouldn't have had launched, even nintendo knows better how to launch a system.
Why the fuck are there so many old men in the game?
Why are there so many young children who doesnt even know how to play a game in the fucking game?!? A game that sold so poorly which was supposed to be a system seller for a sytstem that also sold poorly?
Why can Kirito hack into the game files from inside the game to save data to an item, but on the other hand can't just enable a lookout button again or disable the fucking microwave shit in his netgear?... oh yeah becuase mary sue...

I could write more but i guess i showed why i can't like a show or even respect a show like that especially if there are many shows out there with a similar concept but without sucking that much ass.