Ill throw one, james heller prototype 2.
Now being fair he's not a terribly written chracter on his own, he's a generic action hero that wants his daughter back...The problem is the world around him and the power set they gave him with the story they wanted to tell.
James heller is gifted the same powers as alex mercer...This makes him a defacto man eating abomination against god, he literally eats people to steal their faces, skills and memories. With the occasional snack on other monsters to get stronger. Now short of starving yourself I really can't think of a way to make this powerset "good". At best you might reach a dark nuetral point (only eating criminals/those that "Deserve" it) but they're really designed to be edgy evil powers.
His powers fundamentally don't work with the character the writers wanted and the story bends over backwards trying to pretend heller isn't an abomination.
Most notably three to four missions in we go on a mission to eat a commander, and heller doesn't because he catches the commander on the phone with his daughter...The problem? At this point you've had to eat atleast three or four military personal as part of the story, likely dozens more as you ate the soldiers attacking you for health boost...
The way hellers powers work is he takes everything, name, memory, skills...Everything that made you special as a person gets subsumed and abused by the person that eats you. Are we supposed to assume this commander is the first person hellers met with connections? Friends? Family? Its nonsense the only way for heller to be consistent as a character in that moment is either to eat that man or for him to not have been snacking down on others beforehand.
In the end the real issue was someone wanted a more morally upstanding protagonist but didn't want to change the underlying powers/mechanics from the last game cause they were cool/what made it successful. So we get a man eating abomination against god the story can't ever fully acknowledge is an abomination and will brush aside you eating people as either "they deserved it" OR "We'll pretend that didn't happen"
By the end of my first playthrough I was hoping alex mercer would just eat me, cause as much of an emo bitch as he was being at least he wasn't pretending to be anything other then a megalomaniacal monster with a god complex.
For the flaws with prototype one alex character and his powers were always in sync, there was never a sense of disconnect because in and out of story alex knew he was a monster and reviled and reveled in his nature in equal parts. Hell one of the writers once got @ on twitter about alex barely being better then the monsters/military/black watch and he stated "That was the entire point"
Alex personality and powers were designed around the fact he was a monster, the story worked to reinforce that point throughout the game
Where hellers story trys to dance around what he is and what he does being fundamentally horrifying.