I've played this game enough times to know what are the lows for this game :p

Ok, I have a new one:

FUCK. THE. INVERTED. CASTLE. IN. SYMPHONY. OF. THE. NIGHT.

Yeah I almost always hate it when games put me under time pressure. I play games to relax and that shit just stresses me out and makes me frustrated and anxious.

The real ending is a bit anti-climatic but it's a somewhat interesting ending to the Rondo storyline. Everything up to inverted castle is pretty good. Like you said, inverted castle just sucks. 

The openings to a lot of my favorite RPGs. Takes too long to get to action. Twilight Princess, otherwise one of my favorite games of all time, also kind of falls into this category. I appreciate the world building, but I would like to get to action a little quicker.

The Fanatics' Tower in Final Fantasy VI. If you don't use the Moogle Charm to turn off random encounters, it's a long, slow slog to the top where some of the higher level enemies are capable of wiping you out with a couple of bad rolls.

Persona 4: The first 5 hours. It sets up the story but it's so slow.
The Last of Us: The flooded hotel basement. The atmosphere is amazing, but I'm a coward for horror games and it's a ridiculous difficulty spike.
The Last of Us Part II: Ground Zero/Rat King. See above.
Jak 3: The vehicle section where you have to hunt all those weird monsters in the cave. Also, the boss at the end of act 1.
Final Fantasy VII Remake: Chapter 3. The other open sections are fine enough (though still a big downgrade from the linear sections), but this one is so boring and so visually ugly.
Breath of the Wild: The Yiga Clan hideout mission. It's so annoying as a stealth mission.
Bloodborne: Yahar'Ghul after the blood moon. I am someone who genuinely loved The Nightmare of Mensis for its oppressiveness, but this one was too much.
Ratchet and Clank: Going Commando: The giant Thugs 4 Less robot boss.

I wouldn't mind the intro that much if you didn't have to do chores like fishing for the cat or herding the goats, who thought people would find that fun

Also, everything that has to do with Cerberus and their space ninja in Mass Effect 3. And most sidequests in the Mass Effect games are... not good, really.

The lava jetboard race in Conker's Bad Fur Day. Cool concept but way too punishing.

Spiderball Guardian in Metroid Prime 2. Fiddly, frustrating, and just not fun.

Wing Mario over the Rainbow in Mario 64. The flight physics/controls for the wing cap are garbage.

In Goof Troop stage 5 there's a room with holes in the ground that shift positions all the time and you have to navigate in between them across the room.