There was Eternal Darkness: Sanity's Requiem where you have a sanity meter as well as a health bar, and the more crazy crap your character witnessed the more sanity they lost and the more they would hallucinate. The game even broke the fourth wall just in an attempt to try to screw with your head when your sanity was low (controller has been unplugged messages, things like that).
I'm tempted to go through all of these and throw my two cents in.
"Slow walk communication"
This I feel is somewhat related to invisible walls, unless it's an open-world game. The developers don't want you moving past a certain scripted area but they want to provide the illussion of free movement, so they slow you down to a point where you possinly can't run forwards far enough to trigger the next sequence. In the case of open-world games, I suppose it's just a way to get you to try to focus on the conversation rather than screwing around with stuff, I dunno. We should be able to choose whether we care about the conversation or not, right?
"Highly stylized menu screens" and Orange Deus Ex floating graphics nonsense
This is a problem with graphics design as a whole. Generally you want graphics to give clear information to the player without being intrusive, whether it be a GUI, a menu, or objects in a game world. In Uncharted there was a fairly clear path without making it glow brightly with a 'jump here' symbol. The thing is the whole 'augmented reality' thing is 'cool' so they're trying to find ways to put that into games. Watch Dogs is a big example, where you're supposed to be using your character's cellphone to see all the floating GUI stuff.
Unskippable and flow breaking tutorials
Once upon a time you read the instruction manual to learn how to play the game. Nowadays people don't want to read the instruction manual, they want to play the game, so they plug the instruction manual directly into the first chapter of the game. I remember that Half-Life had an in-game tutorial separate from the actual game, there should be no excuse to have to spend so much gameplay/story on teaching the player basic functionality of the game. It's fine to introduce concepts at a steady pace but we shouldn't need our hands held the whole way through.
Regenerating health
It kinda depends on what brand of regenerating health and the context used in-game. I remember one game where you had health chunks and if you lose a whole chunk it wouldn't regenerate, so you had to use health packs, which is a fairly decent compromise IMO. Assassin's Creed had a 'health' system that I had been imagining for some time, where you only had one or two hit points, but you had a 'composure shield' where doing well would keep the flow going, but as your character/the player struggled to block hits he would lose his composure until he's unable to block them/loses his composure and is hit hard. I think Overgrowth may have something like this but I haven't tried that in a long time. I suppose it's the same principle as a shield, only you'd have much less health underneath it.
No inventory screen
I suppose people feel that inventory screens break the flow of gameplay too much? Lots of games only allow you to carry one or two weapons at a time, for example, because swapping weapons would require you to open an inventory screen, cycle through a list of weapons with one or two buttons, or be playing with a mouse and keyboard.
Needless RPG elements in multiplayer
This is what's known as 'the treadmill'. You might not like playing the game so much, but you have a desire to reach the next level or unlock the next set of gear so you keep playing.
Awful FOV/locked low FPS (Also colorblind mode)
I feel this is primarily a console issue, as increasing/messing with the FOV would require toning the graphics down so the hardware can handle it. Also, colorblindness, it's a thing that actually happens. I'm not affected but it must suck looking at some GUI's and not knowing what the hell is going on. Just have an option that changes a few colors around and you should be set, right?
Long scripted set pieces that add nothing to gameplay
There's lots of instances of the player character doing things during a sequence that is completely impossible for them to do during gameplay. Jumping really high, running up walls, sliding under debris, that kinda thing. If you can't do it during gameplay there had better be a good reason to be able to do it once the controls are taken from the player.
Too many QTEs
I'm not 100% sure how I feel about QTE's. Some could argue that many games are just QTE's where you have to press the same buttons you would in a QTE but you actually have freedom to control yourself. The problem with QTE's is that failing one shouldn't mean instant death/game over, it should instead lead you down a different path or take a chunk of health off. The game shouldn't punish you for putting the controller down during a cutscene either. A cutscene should be a cutscene. Imagine if you put the remote down while watching TV, but the program restarted every time you didn't press certain buttons at certain times. Yeah, nope.
Slow movement speeds + lack of decent sprint
I'd like to chalk this up to the amount of buttons on a controller, but games like Assassins Creed do it well enough that there should be no excuse. Just having a single button on the controller be a 'modifier' button essentially doubles the amount of button presses available on the pad. it could also be a gampeplay thing, though it is still pretty annoying especially when having to travel long distances or get back into a fight etc.
No rebindable keys
There is no excuse for this, is there? I can't really think of a single one.
Lazy level design/linear walling
You have to keep in mind things like Call of Duty and Warfighter are primarily multiplayer games, at least these days they are. It is entirely possible to create linear games that aren't limited and aren't just a corridor.
Bad checkpoint saving
I can't think of a game I recently played that had a bad checkpoint system, it seems to me every single encounter has a checkpoint to make sure that you can get through the encounters. Players should have the freedom to save whenever they want though. I really hate those open world games that require you to move to a certain spot in order to save (save points). What if I have to shut the game off right now? Too bad, all that progress is lost or you have to wait while I walk all the way to the save point and I don't have a sprint function =p
Lack of health bars
This may be loosely tied to the regenerating health issue. Seeing your health bar get close to zero and have it mysteriously fill back up probably isn't as acceptable to people as opposed to seeing the fading vignette. The vignette is more subtle. I would personally prefer health bars though, I like seeing exactly how much health I have. Bonus points if you can enable numbers so you can see just how many points of health you have as opposed to an estimate.
Quest compasses
In a linear game this should be completely unnecessary. In a game where you have something like a GPS I can see it being more reasonable. If anything, more games should have the quest compass point in a direction, but the objective shouldn't be directly on that point. You should have to discover it yourself, or use observation to find it instead of the game taking all the exploration out of it.
Make failure an option
I used to play the demo for Operation Flashpoint back before it came out. I loved that demo, and it only had one or two missions, and yet I remember one of them fondly. You and your squad drive up to a town in Malden and make a downhill assault into it, and then you prceed into the more densely structured area. After that your squad spots a tank column approaching and you have to retreat since you don't have the firepower to take them out. That is, if everything goes right. If all of your squad dies (es they can die, what a novel concept) then you radio to Papa Bear and they tell you to fall back while you can. The game does not abruptly end, you have to fight your way back out and retreat.
I believe there were also branching missions where failure to hold a town meant assaulting it in a later mission, that kind of thing.
Cutscenes
On top of unskipable cutscenes, unpausable cutscenes are a bad offender. If something comes up I should be able to pause the scene and com back later. Huge bonus points if the cutscene has a scrubber and I can fast forward and rewind through it.
Sequels
I'm fine with sequels being similar to their parent games, otherwise they wouldn't really be in the same franchise, right? What I don't like is the game not changing at all or to such a minor extent that there's no purpose to owning the sequel over the original. Sure, stories can continue, but I want some new interesting game mechanics or some feature that keeps me interested during the meat of the game.