Prince of Persia: The Warrior Within put a boss fight within the tutorial.

Although blocking was mentioned at the very start of the tutorial, none of the enemies encounted posed enough of a threat for a player to consider it important. Yet shortly after the player is taught to heal for the first time, they are thrown against a boss where blocking is the only viable tactic.

Novice players are then expected to recognise particular attacks (without any prompting or earlier experience) as the safe point to counter-attack.

What made things worse is that the save point was well before the boss fight, forcing you to repeat the part of the tutorial that had no relevance to the boss.

Forcing a player to read a walkthrough in order to pass the tutorial is certainly not a good experience.

ff6 cid island fishing
breath of fire 3 desert journey
all escort missions

Chaos Strikes Back: How long it takes to reload a save when something goes wrong (which is going to happen a lot in this particular game).

Also, Dungeon Master on the 2gs, if I remember correctly, took a while to load the game each time you boot it. I remember it taking a long time to load, even in comparison to other games of its time.

I also remember that Dungeon Master 2, on the PC my family had at the time, would constantly crash or lock up, making the game not fun to play. (On DOSBox, this game doesn't have this issue.)

GTA: Vice City - RC helicopter mission. Oh man, I never completed the game because of that mission and that was the one GTA that I really liked.

Mafia - Race car mission... It was so frustrating. I did manage to finish it eventually, but it was a harsh experience.

The wall jump parts of Rain World, what a pain in the ass. I never finished the game because of that...

Styx: Master Of Shadow: the "final boss" level, when you need to be agressive in a stealth game.

I can't remember what specific game it was (probably over a decade ago) but it combined two things I dislike and the combination was bad enough that I quit playing the game even though I was enjoying it up to that point. The saves were only allowed at certain points and I hit a challenging battle that I lost. It took most of my play time to get back to the battle that was giving me problems. After a couple times I realized that it wasn't a different tactic that I had to use, but the timing of a couple actions had to be almost perfect. A couple tries later I quit playing the game and never went back to it.

I don't like games that only allow save points a long time apart and I don't like them to be a matter of reflexively mashing the right button at the perfect time. I can handle it if there is some room for error or you can do it quickly again so that you can get the timing down, but the combination of the two made it too frustrating.

Also, I don't think I've ever finished (won) a 4x type game despite really liking them in general. I try to pick a difficulty that will challenge me (may or may not win) but they tend to reach a point where it's obvious I'll win (or lose) but then it becomes a long drawn out micromanagement slog to actually take over the world or whatever. So I just declare myself the winner, quit the game and start over.

Oh, it gets better. For rescue quests, it will generate a new NPC, rather than using one from a pool of active nearby NPCs. This NPC, once rescued is now newfound clutter.

At least there are overhauls like Frackin Universe to fix what [IMPLIED COARSE LANGUAGE] it can.

Reminds me of many video game randomizers.

Example: In Zelda: A Link to the Past, there is a merchant who sells you a bottle for 100 rupees. (Bottles are very useful, as you can fill tem with potions or (with the help of a certain items) fairies.) In the Randomizer, the item you get is randomized so you could pay 100 rupees in order to buy, say, 20 rupees. Does that make sense? (You could also get 300 rupees for the cost of 100, of course.) Meanwhile, some treasure chest in the well in the village has the Silver Arrows (which you're supposed to need in order to defeat Ganon).

Also, that particular randomizer has a "No Logic" mode, which gets rid of the logic (as they call it) that ensures that the game is still winnable. So, now you could have, say, the Ether Medallion placed in the dungeon that can't be accessed without the Ether Medallion, or perhaps the Ganon's Tower Big Key is found on the upper floors of the tower, *after* the point where you need the Big Key to progress.

Yeah, that was awful...

Others that come to mind:

After building your character with love and blood, sweat and tears - none of that matters when you reach the final boss, because this section is played by completely different rules.

Worst game in this regard so far is Two Worlds 2 (base game), where I got so frustrated I actually cheated in the end just to see the final cut-scene.
Another offender is Risen but at least the final battle there is not very hard once you get the hang of it. Still it's really annoying when a game walks over all your player choices just like that and instead forces you to play in a certain way.
Gothic had the problem that the finale only worked as melee fighter or mage - archers were fucked. But that was simply an oversight (game design bug; over-compensated in Gothic 2 where archery was way to powerful against bosses).

Another issue in many games: Escort missions

Too many games to name here, but a good example is Morrowind. The escorted character will happily go after even the mightiest foes with a dagger or even bare fists. Critical characters are not immortal (like in later TES games) and the spawning mechanism makes clearing the way ahead hard to impossible.

Similar are Companion missions. In the much beloved Witcher 3 it was a bit disappointing that while traveling with Lambert (a witcher!) I still had to do all the work. I mean - he didn't die or anything like that (in general NPCs even in the dreaded escort missions are mostly competent enough staying alive - I only got one killed by Rotfiend chain reaction), but it would have been nice if I for one could have leaned back and watch him cut those harpies to shreds. Instead it took ages for him to kill at least one and so I had to kill the rest of the flock by myself.

Believe it or not, I have actually seen a couple games that did escort missions well. In particular:
* VVVVVV: Your escortee moves in a very predictable easily manipulated way, following right behind you when you're on the ground (and the game teaches you this).
* Timespinner has an optional one, but it's quite easy and I am not even sure if your escortee is vulnerable at all. Also, it takes you through an early part of the game that you have been to before.

Such instances are in the minority, but they do exist.

Mafia: Race mission was a game breaker for me. Never did win it, even with patched-in difficulty slider

Clive Barker's Undying: Great, atmospheric horror game for first half; silly, tedious, anticlimactic second half

Planescape Torment: I know that a lot of people consider this a classic RPG game, and I did enjoy some of the writing. But it was much more limited in gameplay options than I thought it would be, making the RPG possibilities very narrow. Baldur's Gate 2 is a much better game in this genre.

Divinity: Original Sin 2: Just played through most of this game. Enjoyed it, for the most part. Got too heavily dependent on puzzles by the end, and was plagued by the "what am I supposed to do next" problem throughout.

Arx Fatalis: Great idea for a RPG, plagued by punishing puzzles.

Mass Effect 3: 40 hours of excellent gameplay ... very disappointing 10-minute conclusion.

Assassin's Creed 2: Parkour fights and jumping across roof tops was fun ... for about 4 hours. Got very old after that.

Star Wars: Jedi Outcast: Overall good game for its time, with solid mechanics and story line. But includes several puzzles that will needlessly cost you hours of frustration unless you resort to a walkthrough guide.

Yeah, I also loved the "Save Princess" quest in Witcher 3 - which actually makes fun of the whole thing (and thankfully is rather short).

Companion gameplay done right can be seen in Bioshock: Infinite.

I remember the opposite situation in The Secret World - there is one mission there where you must escort Carter (a girl with powerful psychic abilities) through the basement. And the thing is, if you have too many enemies attacking, she uses some powerful energy blast, killing everything around, including you. So you must watch her and if you see her preparing for the blast, you should activate personal protection field generator.

Quests where you are given only two choices, that are completely the opposite. Should I allow the family to die a horrible death, or do I give them keys to my mansion since they need it more?

Bullet sponge enemies. Enemy A can be taken out with 1 or 2 hits, but Enemy B is 6 levels higher, so it takes him 20 hits even though they both use the same equipment. A bullet in the lung, is a bullet in the lung. An arrow to the knee, is an arrow to the knee.

Platforming in FPS games. Half-Life's Xen.

The Switch Puzzle. How many times are we going to do the x number of switches on the wall, you must have the correct switches in the on/off position to open the door.

Insta-Kill sections. Mainly where all of a sudden you have a stealth portion, in a non-stealth style game. Get caught, and you need to start over.