I frankly think mentioning Fates characters is unfair, it'd be a shorter list to name actually good Fates characters than bad ones.
Awakening to me doesn't have any egregiously annoying or awful characters, primarily ones that are boring and add little, but Tharja is simply an awful human being who doesn't deserve the love she gets from the fandom. The obsessive girl shtick is annoying, made worse by the fact that in many S-supports she basically goes "Meh, I guess I'll settle for you." to a guy who genuinely does love her, but what takes the cake is her undeniably abusive treatment of her daughter Noire. Fuck Tharja.
As far as Three Houses goes, my two least favourites are Raphael who brings down the entire narrative with his complete lack of character. He literally has nothing going for him other than 'eat food' and 'muscles', oh right, he also has a sister. It just stands out in the worst way in a game with remarkably well-developed characters most of the time. The other is Leonie, who I'm not sure anyone could have thought was likable? Who thought "you don't love your dad as much as I do" was a good personality trait?