There was a thread not long ago called "little things you hate in games". This one is about the big things, or fundamental game mechanics that you can't stomach, but that everyone around you adores. I'll start with a few things:

Dungeons: the staple of every RPG and most action adventures since the beginnings of computer games. Labyrinthine corridors with monotone textures filled with illogically placed loot and a nonsense ecosystem of critters. For some odd reason, torches are always lit, and foodstuffs are never rotten. They can take many forms, but most commonly that of a dreary castle dungeon, absurdly spacious sewers, swamp where your movement is restricted, forest with conveniently cut passages going through it, etc. Sometimes developers get creative, but even if the dungeon is a massive tree bough, it's always the same labyrinthine corridors, creatures that sit tight waiting for you to stumble upon them, and valuable stuff left around. I'll take a logical overworld map or city setting anytime over dungeons, which I consider to be lazy design. Huge sprawling dungeons are even worse because they never seem to end.

Metroidvania style: backtracking and redoing a level I've already completed to explore a small area that was hitherto inaccessible because I lacked a critical skill or piece of equipment? No thanks. When I complete a level, it's done. I want to see something new, even if the game will be shorter for it. Forcing players to redo levels is just unnecessary game padding.

Respawns: when I clear out an area, I expect it to stay clear. In the real world that particular cave or map square will probably repopulate with new bandits and wild beasts eventually, but certainly not in a matter of days. Respawning enemies just make you do something you've already done dozens of times in the same game so it gets boring quickly. Also, it encourages grinding. System Shock 2 was the only game that got respawning right – in small doses, just enough to keep you on your toes. Respawning in Wizardry 8 is just ridiculous.

(Too much) crafting: a great idea at first, but few games have implemented it in the right way. Usually it detracts from the main gameplay, making your character look like a hobo lugging around heaps of junk just in case you need that metal rod, otherwise you'd have to go looking for it.

Large open worlds: the larger the world, the less exciting it is. There's only so much content developers can create. Since they have to populate their ridiculously large maps, that content is always repetitive. How long can you do one activity before it becomes boring and predictable? Also, open worlds tend to mess with quest triggers and there's a host of comorbid problems like level scaling. Give me a small, tight world anytime!

Oh goodie, another topic related to game design.

Anyway, here are some things I hate that many game designers seem to like:

Mini-games: When I play a specific game (or type of game), it is that game's gameplay that I am interested in. If I am playing an RPG (Undertale doesn't count), I do not want to have to dodge bullets (like in a bullet-hell shmup) before continuing. (There's actually an accessibility issue here; someone (especially someone elderly or disabled) might be able to handle the core gameplay, but not the mini-games that the designer decided to put in the game.) Similarly, if I am playing a bullet hell shmup, it would be highly inappropriate for me to have to fight 99 berserkers in a turn-based battle. (Fortunately, the latter hasn't happened yet.)
Exception: If the main focus of a game is mini-games, then mini-games are acceptable.
(Note: Undertale is excluded in the example above because the bullet-hell dodging of that game is part of the game's core gameplay.)

Stealth sequences in non-stealth games: This ruined the Zelda series for me, and is why I haven't played any games in the series past Majora's Mask and the Oracle games. Most of the game, making a single mistake doesn't penalize you that much (except if it involves a wall master; those enemies are obnoxious). However, in stealth sequences, you essentially have to avoid invisible bullets shot by guards, and if you get hit even once, it's like being grabbed by a wall master.
Exception: Stealth focused games are OK, although they aren't my type of game, so don't expect me to actually play games of that type.

Edit: Here's some more:

Anti-grinding mechanisms: Sometimes, I just want to spend time making my characters a little more powerful without progressing the game, and I don't like it when the game goes out of its way to prevent that. (It's one of the things that killed Lords of Xulima for me.)

Cutscenes: When I play a game, I am playing a game because I actually want to *play* the game, not watch a movie. It's the reason that, of all the Final Fantasy games, I consider the original version of the original to have the best intro. The problem of cutscenes gets even worse when they are unskipable, especially when they involve load times (which makes me nervous if the game is running from a CD).

Skill point systems: In my experience, I have decided that the common (these days) RPG mechanic of getting skill points to allocate at level up has its flaws. It increases the number of irreversible choices that have to be made to an unreasonably high amount, and it discourages generalist characters. (Very few RPGs get generalist characters right.) Exception: If there is a practical infinite source of skill points, this problem isn't as bad; for example, in Avernum 1 and 2, the money sink of buying out a certain witch's inventory to get more Knowledge Brews. (A money sink is a mechanic that provides a use for all that excess money you have near the end of certain games.)

Dunno if a feature... but attacks of opportunity in turn based games.

To avoid the giant slalom during movement phase, they often resort to this horrible "feature".
Bad system design.

Random combat encounters.
Especially with an annoying transition effect.

I can't think of anything that I hate that most people seem to like, but there are a few things I'm not that fond of that a couple of people seem to like. ;)

Cities

Cities can be an exciting place for adventure, but in most games they aren't. I often find it pretty tedious to "explore" the site by talking to citizens, merchants and officials, and they seldom have anything to say I find really interesting. I'd rather explore the wilderness again. Or a ruined city without any merchants to talk to. :P

Realism in games

I don't care if this merchant needs to sleep at night, if he has only 1000 gp to spare before he's broke or if he's only interested in cloth and not metal, I just want to make a quick coin, get rid of the useless stuff that's clogging my backpack and be off to adventure again. I don't care if carrying 10 greatswords in my small backpack is suddenly considered too heavy, while sticking 9 into it was still perfectly fine. I don't need the game to remind me that living beings need to have food, sleep, bowel movement and whatnot, unless it's really well integrated into the gameplay and actually fun to simulate. ;)

Branching paths in story-oriented games

It's pretty cool when a game reacts to your choices, no doubt about that. It would also be pretty cool if your second playthrough was different enough from the first one to feel totally fresh again. But I hardly ever experience that with games I play. They seem more like a compromise in that regard; up to 30% new, 70% same old same old. And that's not enough for me to want to play through them again. So it's nice when my choices do make enough of a difference to make me feel like they matter, but I don't like the thought of missing out on bigger chunks of the story or the areas unless I replay the game (and deal with all the repetition).

Boss Battles

I do admit that they can be fun, and that they can feel satisfying to beat, if they're well done. But more often than not, I don't look forward to them and I'm glad when they're over. They often break the flow of the game by replacing the usual mechanics with something else, because the usual stuff suddenly stops working, and then they're more of a puzzle with you trying to figure out what the game wants you to do, or the bosses are ridiculously overpowered compared to the trashmobs you had to deal with before, and it takes ages to beat them. I don't know if I'm just impatient or if many of these really aren't that well designed, but I always expect them to be more trouble than fun.

That being said, I like dungeons, despite understanding the OP's reasoning, just for the atmosphere of dark corridors and torches and stones; I like the Metroidvania feeling of "Oh, now I can also go there, if I want to", but I agree that backtracking shouldn't be exaggerated; Respawns depends on the game, generally I like that sense of achievement you get after clearing out areas; Crafting I mostly ignore, but I don't mind it being there; Open Worlds are great, but yeah, they can get boring or overwhelming if they're too large. I'm fine with skill point systems, cutscenes, and a lack of grinding opportunities, although I can see the latter leading to problems occasionally; mini games are fine in moderation and depending on their type, they can get annoying quickly though; and Stealth is something that I often love to do when it's not required but hate when it's compulsory. All in all I guess I can see both sides in most things.

EDIT: Oh, yeah, Random Encounters, don't like them very much.

Multiplayer

Re-spawning

Personally, I don't mind random encounters. The most common alternative, which is visible enemies moving in real time, however, I *do* mind, at least in games with turn based combat. When I am playing a turn based RPG, I do not like it when the game turns into an action game.

Note that Zelda 2 doesn't have this issue, because the game doesn't even pretend to be a turn-based RPG. Personally, my problem isn't the idea of boss battles themselves, but rather two thing that often happen:

1. The game focuses on boss battles at the expense of normal encounters. In many RPGs, normal encounters just aren't interesting, because all the attention is placed on the bosses. (Wizardry 8, which I have been playing lately, handles this much better than most RPGs, though the game isn't perfect.)

2. Boss battles are usually not repeatable. If I just want to have fun, I typically can't just go back to the fun boss battle I just played through and replay it. (Other non-repeatable parts of the game suffer from the same issue.)

Exclusive use of check-point saves. This damn near broke games like Oni and Halo for me. Especially Oni, where I'd get though a gruelling fight only to get killed by some BS trap in the level.

Would you rather have a "menu town"? :p Large cities can be overwhelming, both for myself and my hardware. :) But smaller towns work rather well if everything is clustered in a small area so that there are no unnecessary loading screens. Towns/cities are usually great safe places to unwind after an adventure in the wilderness.

Which brings me to another point... NPC schedules are often praised, but they can be rather annoying. Especially when you need to buy that one item, and you arrive mere minutes after closing time. Or you chase a specific NPC around a city when you just want to turn in your quest.

Dunno, in some games, maybe. But preferably smaller cities with more interesting characters in it who can tell of exciting things without making too many words. And like you say, everything clustered in smaller areas. Some cities are huge but lack the content to fill all that space. E.g. I much preferred the smaller but distinctly individual towns of Nehrim to the first big but boring city in Oblivion. And what I don't like about cities is that they often seem to slow the game down in RPGs. I don't mind a little unwinding when I feel like it, but in many RPGs cities are a compulsory part of the story progression, e.g. Act 1: Wilderness, Act 2: City Exploration, and in those cases I often lose a bit of passion and motivation when I know next up is lots of running to and fro, talking with citizens, snooping around in houses and trash cans and boring fetch quests. I do like city architecture though, so if a game cuts down on all the mundane stuff and concentrates on mystery and adventure within the city walls, that can be fun, too.

I don't particularly like unoriginal High Fantasy.
I don't like Dungeons like the OP described.
I dislike magic that inflicts HP damage.
I hate it when a game ignores the logic of its own game world. That's something you wouldn't accept in a book or film, why accept it in a game?
I hate everything about Skyrim.(Well almost everything) ): !? D:

Games that are hard: When I play games I do it for the story or because I want to relax, not to keep dying over and over or failing missions/levels just because I don't happen to be the best player ever. I want games that have a good story and that have an easy playability.

RPG ... I still can't get into this genre.

1) RTS. I play chess, not dodgeball.

2) Shooters. First-person POV. First-person shooters.

3) The "fog of war" mechanic, especially in space battle sims.

4) Time limits, random events, or anything else that takes away from the "strategy" part of TBS.

Just let me play my game, my way, at my own pace. Oh, and get off my lawn!

Did my preferences make you speechless? ;)

Those headings are admittedly a bit vague and misleading. I don't actually dislike cities or realism in games, only "mundane city chatter and errands" and "meticulous real life simulation in games that are not part of the survival genre".