An anti-feature is a "feature" that the game (or other thing) would be better off without.

For purposes of this topic, please only discuss anti-features of the game design itself, and not things like DRM (which is an anti-feature, but it's not the point of the topic).

What anti-features in games are more common than they should be?

Here are two that I can come up with:

1. Punishment for death. Some games penalize characters who die with things like aging or permanent stat penalties. These penalties simple serve the function of encouraging players to reload rather than accepting the death and continuing on. The player already has to repeat a section or play down a party member or spend resources on revival; you don't need to punish her any further.

2. Genre switches. When someone chooses a game, that person chooses a game of a genre that she wants to play (and is able to). When the game switches genre, you end up in a situation where the player must get through a part of the game that she hates to get to the good part of the game. One example is stealth sequences in non-stealth games (like modern Zelda); another is action mini-games like the ones in Final Fantasy games.

In the cast of example 2, some players may not even be able to pass certain points. Putting action in a turn-based game, for example, causes problems for disabled gamers who can't press buttons fast enough to go through action games. Putting a turn-based sequence in an action game (which is far less common) can be an issue for young children who don't know how to read.

3. Invisible level transitions with auto save and no way to go back. I really hate them. I'm looking at you, Hard Reset.

4. Taking away control from the player to show an endless stream of irrelevant, boring and unskippable cutscenes. This is especially bad in combination with 5.

5. No manual saving and badly placed checkpoints.

The worst offender for a combination of 4 and 5 is Warhammer 40000: Space Marine. Unskippable cutscenes after checkpoints. Watch the cutscene, die and repeat.

Saving only in very specific locations (inns) and autosaves. I don't like feeling pressed by time and fear that 2+ hour session might be destroyed by power outage or mechanics, which cause sudden total party wipe (and autosave/delete my saves). And currently I found myself doing some work, relaxing a bit by 10-15 minute gaming session, then back to work again. It gives no time to progress anywhere in game without real saves.

This reminds me of a part in Final Fantasy X (which I haven't played, but I have seen the part in question on Youtube). There is one part where there is a 5 minute unskipable cutscene, followed immediately by a 3 phase boss fight. If you are playing rationally (i.e. curing status ailments that you are afflicted with) and have not fought the boss before, there is a very good chance that the attack the boss uses at the start of the third phase will wipe out your entire party, forcing you to reload and watch the entire 5 minute cutscene *again*.

Final Fantasy 5 and Final Fantasy 4 DS handled similar situations better. Both those games have a trick battle where death is likely and where there is a cutscene, but fortunately, the cutscene comes *after* the battle, not before. Therefore, if you die (and in the 4DS case, if you had the foresight to go back and save after the previous battle), you don't lose much time.

Trick/puzzle bosses like these can be done well, but the developer needs to make sure that failures cost as little of the player's time as possible.

Similar to your point 3, invisible events in a dungeon (far away from a save point) that force you out of the dungeon, causing you to miss treasure inside.

Invisible walls

QTE's

Zombies

Mandatory grinding

5 minutes is nothing. Some cutscenes are 10+ minutes long, with Luca and Guadosalam being the worst offenders. And Lady Y. was very easy boss, people had problems with her only because everything up to her was complete faceroll, and she actually tried to resist the onslaught. Game is actually quite good, if you manage to survive endless cutscenes until Calm Lands.

I remember Phantasy Star II bosses, when you had to go through quite long maze, open Pandora Box and probably die over and over again, and then having to go through:
1. Ice plains.
2. Underground caves.
3. More ice plains.
4. Actual dungeon.
And you had to fight everything on your way to boss, because escape chances were very very small :) 5 minutes is really nothing :)

Yes. And no software is without bugs, so there is the possibility of crashes, too.

I, too, like games that I can pop into, play some time, save and get back to what I was doing. One of my friends I almost always late and it's nice to be able to play something until he arrives. Impossible without manual saving. And no – casual games aren't the answer! Absolutely. There is absolutely no good reason for unskippable cutscenes to begin with. Most of the time I replay a game, I know what happens in the cutscene and I don't need (and want) to watch it a even a second time. Really annoying in combination with slow walking speed in first/third person games. Torchlight and, again, Space Marine are the first examples that I can think of.

The problem with Lady Y., from what I can tell, isn't the boss being a challenge, but rather that the boss has one attack that will likely cause a party wipe on the first attempt. Of course, the boss is easy once you realize how to survive that attack, but you won't know that on your first attempt (unless you happen to have looked it up).

Also, Phantasy Star II has the Visiphone item that lets you hard save anywhere. If you lose to a boss, just reload the save from right before the boss. (Also, don't give it to Nei.)

Another anti-feature: punishing the player for progressing through the story. Final Fantasy 7 is one offender here: after a certain point, the game doesn't let you use the character with the most interesting limit breaks in your party.

Unskippable cutscenes or unskippable NPC dialogue (I'm looking at you Legend of Kay). Made all the more egregious if a checkpoint is placed before one of them.

Escort missions. Does anyone actually enjoy babysitting drooling AI? Or protecting said drooler while they mend/hack etc?

RPGs where the lack of balance or natural progession forces you to mindlessly grind levels. Or conversely, RPGs that scale the enemies based on your own level, removing any real sense of improvement.

Thing with Visiphone is that it was rare steal by Shir. If you know Shir - she was nigh useless character, and she liked to regularly leave your party (to steal something). I'd say it is problem with all games, which have fluctuating parties. Final Fantasy IV: Edward, Palom, Porom, some other peeps leaving or dying. Dragon Quest VII: Kiefer leaves (Maribel also goes AWOL for looong time). Those are the characters, in whom you are likely to invest quite a lot.

Subversion can be seen in Baldur's Gate. If you will ignore quests of your party members, they will leave. Easy to screw yourself by saving shortly before they leave, and having hard battle in front of you.

All these party shenanigans are quite bad...

You would love Ravenloft's vampires.

Procedural generation. It's an interesting little feature that sometimes works well enough, but it never has and never will replace meaningful level design. Indies in particular seem weirdly obsessed with it.

People already mentioned QTEs and unskippable cutscenes, but in combination too...having to do some QTE and then have it followed by some boring, long and drawn out "execution" cutscene. It might be "bad-ass" to watch the first or second time, but having to go through them hundreds of times gets old really fast.

Add this one to my list. To me procedurally generated maps generally translate to 'everything looks and feels the bloody same'.

An autosave function in a stealth level that saves after the alarm is raised and you have to restart from the first checkpoint. Metro 2033, LL.