i posted about one of them, but might as well mention more
1. mass effect 2- mining. wouldn't be so bad if there was any way to tell what minerals were on a planet. but you cant, and the most popular minerals arent used as much as the others, and it could take multiple planets before you find any with a significant amount of what you need, with no way to tell that until youve mined the entire thing.
2. wind waker - sailing before you can warp. while sailing was fun to explore, it wasn't fun when you had to travel to continue the plot and then spent six minutes doing nothing
3. world of warcraft - flight paths. this isn't nearly as bad as it was, back before burning crusade. in vanilla wow the two raids everyone did, and which most guilds never got out of/stopped doing except for the very top, where located in black rock mountain. for the horde, the only way to get there was kargath, a town that was way far away from anywhere else. to get there from undercity was about nine minutes for a flight path, where you did nothing. from grom'gol to kargath was about four minutes. but to get to grom'gol you had to take a zeppelin from orgrimar/under city, and if its not waiting for you then you had to sit and wait for minutes before it came up. a lot of people set their hearths to kargath, but then you had the same trouble distance to get to any important city to trade/do battlegrounds.
4. dead rising - saves. oh god the saves. it was a fun game, but nothing stopped replaying it as much as the save system. you can only save in the few bathrooms, and when you die you start over from that save. which isnt that bad, except that theres a time limit for most things, so you dont have time to just go to every close bathroom and save before you do stuff, plus zombies are literally everywhere which makes it harder to save. also, the end game if you get an A rating- no zombies, just guys with better guns then you, so you have to shoot them. except you cant move and shoot and the aiming thing is slow.
5. gta: san andreas- the driving. it takes soo god**** long to drive from one city to the next, which isnt that bad since generally you only do missions in one city at a time, but then there are missions where you have to drive to the country side. thankfully a lot of them have it where if you die you start up at a certain point, not at the hospital/safehouse like normal, but thats still a lot. also, the plot sort of breaks down once you leave your homecity. its not that bad, but its harder to believe/care about the story when your character goes from being a ghetto talking gangster to being a ghetto talking guy who helps out the elegant chinese triads and some silly nerd guy who has you fly model airplanes for him.
6. gta iv: swimming. generally not bad unless you fall into the water at some point, or accidentally crash into it, but ladders to cut up aren't as common as they should be, and boats are incredibly rare. not nearly as bad as any other thing on this list, as its generally at most a one minute thing, but it gets annoying. honestly boats dont really serve a purpose in the game except for a handful of missions where you drive one, as you never have any reason to get on a boat outside of that, and even if you wanted to drive away in a boat from the cops you probably cant because there are so few boats. more of a nit pick, though.
7. any game where you have no idea what to do next - this is probably the worst thing in any video game. i don't mind hard puzzles, or having to search for stuff, but when you have literally zero idea on what to do its not fun. first game that comes to mind for me is jedi outcast. so many of the missions require you to do some sort of puzzle at random points to advance, generally a sort of platforming thing, but you never have any idea about it until you realize you cant go forward. plus a lot of missions have you reach a dead end, then just go back and go a different way, and the puzzles are almost never obvious. its even worst in missions where you drop down into an area, then after clearing out several rooms in a general area have no idea which room would possibly be the one where you have to do something to advance, and you wouldn't know if it was until you actually do it.
8. red alert 2- commando missions. for those who dont know its where, in an rts game, you have a mission where you're just given a single infrantry man, a commando, and have to infiltrate a base/blow something up. these are actually generally fun at times, but are also incredibly frustrating. for one thing, a lot of the commando missions have you start out with a commando, then have you find a "base" where you then go to normal rts stuff. but if your commando dies at any point in the mission you lose, even if you're crushing the enemy base, so after you don't need your commanod you generally just leave it in your base. the main thing, though, is dogs. dogs kill any infantry, even commandos, in one hit, and move incredibly fast. your commando might be able to kill ten units at a time, but a pack of three dogs will murder you in a second.
9. games where they take away abilities for a mission - the only good example of this i can think of is half life 2, where at the end you lose all your firearms, but your gravity gun is instead capable of killing people. in general, though, the more abilities you have the more fun the game is. taking away abilities for a mission is generally just a cheap way to increase difficulty without them actually designing a hard level thats fun. missions where you jail break and have no items on you (a lot of games) can be fun, but only if the part where you don't have your items is short, like escaping, then going through a hallway or two to get weapons. for example, max payne 1. you got captured, and then escape with nothing but a baseball bat. but in the next room is a hallway where you have to sneak around until you find a group of enemies that are small enough that you can murder with your bat before taking their guns to actually fight, and within about ten minutes of breaking out you're already back to how you were before.