Any forced stealth section in a non-stealth game is this for me

Really? I never minded those and generally considered them like a quick cash inflow since I generally finish those quests with a quarter of the watch to spare

Cid minigame from Final Fantasy IX comes to mind first.

I don't recall ever having any issues with water levels, loved the one in OOT.

Sections I don't like in game, boss fights, pretty much all of them except SotC (those are more puzzles) Boss fights are just annoying obstacles to me, only RE7 in VR gave me some satisfying boss fights.

Hate is a bit strong, but...

FFX - Blitzball

Dragon Age Origins - The Fade

Also any instance of forced defeat battles and any instance of character cutscene incompetence.

Carnival Zone in Sonic 3.

Ocean Palace in Zelda Phantom Hourglass.

Mementos in Persona 5.

Sometimes I feel like I am the only one that enjoyed Blitzball in FFX.  Mind you I was in early high school at the time where the net was still in infancy, so when a bunch of friends from school and I used to talk Blitzball and who we were recruiting...it seemed like a smash hit mini game at the time it wasn't really talked about on forums back then.  We used to love comparing team stats and theorize who would win in a legit PvP match based on our skill and recruited members of our team.

One thing I dislike very much is how in Persona games, if your party characters are KOed, you can bring them back through various means, but if the main character falls in battle, then it’s an instant trip to the Game Over screen. None of this being supported by in-game logic of any kind. Just the game designers being morons.

This made my treks through Mementos a chore in the later parts of the game, and I have put the game on hold for a long time because of this stupid and frustrating design choice. 

If it made sense from a plot perspective, fine, but it doesn’t. It’s just there “because”, just like so many other aspects of the series. 

Honestly, I don't get the hate for The Fade. Doesn't The Fade also include the dungeon where you turn into a rat and have to gain different forms in order to beat the dungeon? Seemed pretty cool to me and I liked how you had to go back to the earlier parts of the dungeon to progress at times. Doesn't The Fade also include the part where you have to talk to each of your party members and you see their dreams and desires? One of the coolest parts of the game too, imo. 

Really the bigger problem Origins has is just how shit it's pacing is when it decides to constantly throw enemies at you in it's dungeons, which I guess The Fade does sometimes, but I seem to remember it being more creative about it then the normal dungeons. 

I played Super Metroid for the first time last year, and honestly I think Maridia is just not super well designed. It's actually easy to navigate 99% of it - the issue is that the part you need to go for Maridia for is hidden like it's some super secret energy tank. That's a problem especially when it's so close to the end of the game (for a normal playthrough), just dampens the pacing I think. 

I love Banjo Kazooie but Mr Vile the crocodile is frustratingly hard for only being in the 4th world; it was the last Jiggy in the entire game I got.

Love Skyward Sword, but the Imprisoned is annoying enough once much less three goddamn times.

Love Starfox, but the two secret levels were a big letdown, just uninspired and boring.

Love Dead Space, but that motherfucking turret section is so horrific it almost single handedly makes me never want to replay the game despite it otherwise being one of my top 10 PS3/360 games.

What makes it worse is that the canon sequel (Persona 5 Strikers) does allow Joker to be KOed, further confirmation of what you said.  It has no relevance to the plot what so ever.  There have been a number of times I saw the game over screen simply due fluke status effects and a focus on the MC from every enemy attack.  They were not even particularly hard encounters either, as it was never hard to take them down otherwise.  It was utter BS and felt lile the game was just giving me the finger at those times, as there was nothing I could do to stop it once the sequence had started.