This topic basically encapsulates every waifu and husbando ever, if a game gets a lot of attention you're gonna get mixed receptions. Also understanding how controversial an opinion you have depends on your understanding of general opion.
That said, for Reborn, Titania can fuck off and Fern, Fern's a dick but that's about it, and I like Dicks.
Gaming in general is harder, I'll go for two big series I guess so I'm not just plumbing vague feelings. I don't have many franchises per se that really stick out to me though so Kh and Persona it is.
KH:
I adore Roxas in spite of the incredibly long tutorial he was in KH2 that seems to really irk a lot of people. That said I played his game 358/2 before I did 2 because 2 was damned hard to find for me, meaning I went into 2 understanding his shtick and with a healthy attachment to him by dint of spending 40 odd hours with him. It's harder for me to dismiss him as an edgelord as well when he shows up at other times too because his story is genuinely tragic. Good boy 10/10
Riku: I get his character arc, I understand his bit, maybe it's the imo flat voice acting or just the fact that his Hollow Bastion fight in 1 fucked me up for ages but I don't really like the guy. I also never played CoM because fuck that battle system in its entirety, so I know I'm missing out on a good chunk of his screen time.
Sora: I like him. He is very much a flawed protagonist, not the brightest, consistently put forward as a linchpin character, we're almost forced to like him and enjoy him over other more interesting and nuanced characters and, for me, it works. Dude wasn't initially the main character but solely through being a nice guy he manages to step up to the plate and do the damn thing. I appreciate that.
Persona:
Junpei, Yukari and Mitsuru: So these three made up my main party in p3 right up to the end because I like to spam healing all the time and I liked Junpei more than Koromaru. Tactically they jsut made sense for me but of course most of the reasons theya ren't too well liked lies mostly in the story, at least for the first two. I never suffered from Mitsuru's charm fuckery too much.
So people dislike Yukari, afaik, because of the Answer wherein she becomes a fair bit more "bitchy" as has been said to me. I never played the answer, the main game felt comprehensive enough and I just never got around to it. So my experience of Yukari was just her main story and her Social Link. Honestly, one of the best Persona girls, she was my romance in 3.
Now Junpei, he's different, people don't like him because of his role in the main game. He starts off as an ego driven show off who resents you for being perfect, because you're the mc of course you're perfect. It might be an illusion on my end but it seems like a lot of people discount just how much personal growth he goes through, going so far even as to have his own relative side story that builds his relationship with an antagonist completely independently of the MC, this really stood out to me in a game where it felt like everything happened based on the MC taking action and pushing forward the story and I ended up adoring my bro for it.
Naoto, Chie and Yukiko:
Naoto i'm just not keen on because I stopped playing in the middle of her dungeon. She jsut wasn't compelling enough for me to care and I ended up fading away from the game. Fairly light reasons to dislike her.
Chie, maybe it was just her inital voice actor but good god she was grating and her focus on phsyical skills in the original, bear in mind i was emulating the first and not playing golden, was just meh.
Yukiko though, oh good god, everyone seems to like her and find her adorable and gorgeous and blah blah blah blah blah when pretty much all her traits aren't the least bit endearing to me and her character design feels so very flat. She looks like she could be an npc with a red coat, not this gorgoues idol the game keeps pushing her as. I dropped her asap and I ended up running an all male team in P4 before stopping, despite hating Teddy.
for P5 I don't really have a grasp on who's a controversial character, maybe Ann and Ryuji cuz Ann is the secksy won and Ryuji constantly gets shit on by everyone in game, I like just about everyone in that game though so I'd basically just end up defending people when idek the issues people have with the characters.