I’m gonna preface this by saying that this is just my opinion, and that I might be wrong about the game I’m going to talk about here. I know it’s very beloved by the community, but I just couldn’t get into it. 
So, two ROs that I didn’t like were Ortega and Mortum from the first Fallen Hero game. But I think “Didn’t like” is a bit of a misnomer, because I really felt kind of indifferent towards them for most of the story, and then increasingly frustrated as they started showing up more. I think one shortcoming there is that it feels like the game has a very specific idea in mind for how your character is supposed to relate to those two (the MC is melancholic and distant towards Ortega, and intrigued by Mortum), and anything outside of that makes the story feel a bit clunkier, so, even if they are very proeminent characters in a long story, I just can’t get into them at all.