A few off the top of my head. I can guess at the good intentions behind most mechanics that people, including me, don't like, but there's definitely some I think are done poorly but could have been great, and some that just aren't that good a fit for the game (or even the genre) in the first place.
'RPG reserve party members don't get xp' (good intention: cycle through characters to explore their abilities and change up combat)
I've always preferred games that have reserve units have an xp cap that equals lowest level of active member-1 or something like that. Otherwise, if the game expects me to spend hours grinding levels of extra units, on the off chance they throw in the next point for a single hour of play or the final boss, my heart just sinks. Which brings me into...
'In a 50 hour RPG, you need to use your underlevelled, underequipped, reserve party members. But for a boss fight' (good intention: sense of unity, of all reserves being part of the team)
If it's the final boss, and the game has given no indication they plan to do this, by having no requirement to level up and buy equipment for annoying reserves through an early section showing it, I'll likely just quit and watch the ending on YouTube. This brings me into...
'Strangely large party size combined with the above points' (good intention: epic feel of heroes from all over the world forming a force capable of great things)
It's good to have, say, the same number of reserve choices as the active party. I like it when RPGs have characters rotate in and out of the party due to plot requirements as it usually means character development other than for the 'chosen one' hero. But if there are 3-4 active members and 2/3 times that in reserve, then those reserves are also more likely to include a number of irritating tropey characters, on top of any idea of levelling up and keeping them equipped appropriately going out the window unless you want to grind.
'Very easy puzzle sections in games where you are playing as a competent adventurer' (good intention: pacing, making players feel smart)
I like environmental puzzles in games. The moment an RPG dungeon puzzle 'clicks' is great. But when, like Skyrim or Uncharted, it's so simple that it's an ancient tomb thwarting adventurers for centuries before the player can solve it in two minutes of trial and error, I just shrug. Any idea of sombre/oppressive atmosphere of ancient locations lost in the fear that pacing is one thing but heaven forbid that the player hasn't stabbed/shot a generic mercenary in the last two minutes.
'Poor stealth sections in non-stealth games' (good intention: varied pacing, get player to slow down and appreciate detail of environment)
I don't mind these when done well, but often they lack audio and visual ideas of what enemy guards/cameras can actually see, making it trial and error as the only feedback you have to learn from is an instant fail state. I like it when the game gives you vision cones for enemies or a meter showing how much noise you are making or something like that. At that point it's a puzzle as you have some info to work with. Otherwise I just hope it's relatively short.