After thinking about how I myself would answer the topic, I actually came up with a fair number of boss segments that I remembers finding quite bad for a variety of reasons.
Hoffman | Rule of Rose
Rule of Rose is notoriously known for its awful gameplay and controls, and it's abundantly evident and at its worst during the game's first boss fight. Whereas the player must be facing toward the boss at the perfect angle, the boss has a wide-range reach that's difficult to avoid and is even used when countering player attacks.
Munakata Seishirou | Yakuza 4
I don't actually remember if I needed to try this boss fight more than once, but I remember it being so irritating. All around, lesser enemies in large numbers surround the player while the actual boss runs in circles shooting bullets at you. If you go after the boss, he runs away and the enemies bombard you. And if you go after the enemies, the boss shoots. Who the player controls (as there are four protagonists in this game) is the one with less efficient combat design, so it makes this sequence far more difficult than it should be.
Orochi | Ōkami
While I don't particularly remember if this boss is even difficult to defeat, what I do remember is that it's required to fight them on three separate occasions that are nearly identical. It's one of the several reasons Ōkami is, in my earnest opinion, a bad game.
Sakura Head | Silent Hill: The Short Message
While not a boss in the traditional sense, this gameplay sequence is far more offensive than it should be. What should be a relatively simple chase sequence is anything but, as players are forced to navigate through a labyrinth of rooms and corridors that prove challenging to differentiate on its own, and especially when being chased by a monster. In a moment's notice upon turning a corner or opening a door, Sakura Head may suddenly appear. And when the distance between you too gets too close, it's an instant fail state. For a 2–3 hour game, this segment took me about thirty minutes alone.
Sephiroth | Kingdom Hearts
During the PlayStation 2 era, I played through Kingdom Hearts a lot. I've never been able to defeat Sephiroth once. I think the developers realized this once designing the sequel's boss encounter with Sephiroth once more, as it's a considerably much easier fight (meaning I was able to beat it, at least.)
Seymour Flux | Final Fantasy X
It's been twenty years since I've played through Final Fantasy X, but I remember having to initiate this fight time after time after time again. Besides the sharp spike in difficulty occurring, what makes this segment unbearable is the extended cutscene preceding it that can't be skipped. I'm sure there are ways to make this fight easier if knowing about it ahead of time, but it was quite a challenge for me as someone playing the game for the first time.
Shadow Okumura | Persona 5 Royal
Annoyingly, numerous waves of enemies that progress in difficulty must first be defeated before actually fighting the boss. And, even worse, the enemies in each wave must be defeated in a certain amount of turns (and ideally all at once) or else they flee with new enemies from the same wave type spawning in their place. Throughout it all, there's a lot to balance with main boss acting from the sidelines inflicting buffs on enemies and de-buffs on player's party. And what's worse is that this fight has a strict time limit. It's not unbearable after a few attempts or knowing what to expect far in advance (as there is also a sharp spike in difficulty), but it's such poorly-designed fight.
Wizpig | Diddy Kong Racing
The final race against Wizpig is often regarded as being quite a challenge, and that's how I remember it too. I never was able to finish the game when I played it years ago, but I'm curious just how difficult it is since I've forgotten and would probably be more skilled of a player now than I was then. From what I've seen, it's a race that requires near-perfect play and course memorization. I'm also now learning that there's actually a second race with Wizpig which I'm reading is just as difficult if not more.
