Here's a small list of stuff I don't like, and for some of the things, I offer some insight on how to improve from these, making them less irksome and more enjoyable.
1. As someone else mentioned before, battles that you win, but the scene afterward it shows you actually lost. If I want a 'But thou must' scenario where you lose in some way, then I will at least have the characters (and the player) have a moment of victory, maybe even gain something useful, even if they didn't get the plot coupon.
2. Unlooped loopable music. Not music that could not be looped due to the structure of the music, but music that could be looped well enough by messing around with Audacity. I draw the line of tolerance just after looped music with a slight skip. That is justifiable due to inexperience or the music sample not having a corroborating note or beat. If your final boss has, for example, 'Roar of the Departed' from Lost Odyssey and it's not looped, the exciting music will suddenly be interrupted by a few minutes of operatic singing that ruins the mood. (That is an extreme example, but there are people who would be inexperienced enough to do it.)
3. Wrong use... of ellipses... is important...
As I just demonstrated right there, awkward timing in pauses can cause a form of irritation that is as caustic to the mind as it is to the enjoyment of the game. To those who use ellipses, remember to read the line out so that it sounds natural. This will segue into 4. Bad Writing, and I will speak of both at the same time.
When writing, dialogue is very important. The characters must sound realistic, unless you are not really trying and/or are writing the base plot for later revision. Reading out loud the dialogue, or acting it out, helps immensely to prevent dull writing. Punctuation is also a must, as it can convey feeling. A simple comma for a short pause, such as the pause before 'such', prevents the player from thinking everything is one long fast-spoken sentence. Ellipses... They can be used to trail off or to indicate careful consideration of words spoken. I will provide an example:
"Maria... I... I don't like this..." This is overuse of ellipses.
"Maria, I... I don't like this." This is proper, the comma gives the right amount of pause, the pause after 'I' suggests hesitation, and the period at the end is proper, giving the sentence finality that the previous did not give.
But, I must digress, else I will turn this into a long lecture on proper sentence structure.
5. Badly used cliches. Cliches are not inherently bad. You can make an entire game with just cliches and have it be enjoyable, if it is done right. However, using cliches just so you can make a story and say, "I made a story, so I am automatically an awesome writer/game designer/et cetera!" does not work well.
6. Gratuitous tropes and obvious/surprise twists. There are tropes that are prevalent in many works, and knowing them can be beneficial. But when you're trying to incorporate every trope under the sun, and the game is not the more enjoyable for it, then you've failed, unless it was your intention to fail. Tropes are tools and are not bad, but being trope overdosed is.
The same goes for twists. Twists in a story are _____ hard. You have to lay out a lot of subtle foreshadowing and make sure that the player can notice them, but without anything blatant. Say you have a character named George. George is the designated hero and is trying to stop Emperor Evil. If you are skilled enough, you can write the story so that some similarities between the character is noted, so that when the twist comes, George learns that he is the son of Emperor Evil.
Now, this example has a spoiler for Bioshock 1. If you have not played it, then I strongly advise you to skip to the next paragraph.
In Bioshock, you are able to gather some audio diaries that, initially, don't seem to do much except build the world of the game. However, the diaries, in conjunction with dialogue with a character named Atlas, hint toward the game's twist, which is a double whammy. That you are the son of Andrew Ryan, the game's big bad, and the mind-controlled puppet of Atlas, who turns out to be Frank Fontaine, and was ultimately meant to kill Andrew Ryan.
This is an excellent example of a twist.
But, when you're able to see a twist in-game from a mile away, or there is no foreshadowing whatsoever, then it doesn't work.
7. Blatant padding. Such as, multiple fetch quests that expand the play time of the game to long hours, luck based missions that require save-scumming and have no alternative way to beat the mission. Things such as these are abhorrent and are better left elsewhere. However, if you can make these enjoyable and fun, then you are closer to being awesome than most people.
8. Escort missions. These are the absolute worst, but can be done properly. You are given a character and are expected to keep them alive, no matter the cost. If they die, you have to start over from the last save. Two RPG examples of escort missions that are tolerable, if not downright fun, are the Banon EM, and the Liem EM from Final Fantasy 6 and Terranigma, respectively.
In FF6, Banon is given a skill that heals the entire party, but if he dies, it's game over. This is tolerable, even during the Ultros battle, because the skill is free to use, and if you didn't run from every encounter, the battle shouldn't be too difficult.
In Terranigma, you must rescue a lion cub named Liem from a deadly trial. The little cub views it all as a race between him and you, he runs ahead, but you often catch up to him and help him through some simple and short mazes and protect him from weak monsters. During this, you have 'Willful Lion' playing in the background, with is just awesome. At the end, you face a boss you eventually cannot beat and are trapped on a ledge far below the boss. Liem, in turn, fights the boss by himself and saves you.
If you want an EM in your game, make sure it's not frustrating, strive for fun and awesome.
That's about it, for now.