To use a recent example of controls annoying me, I played Mass Effect 3 recently on the PC and it had multiple commands bound to the one button and gave me no way to change it. Look I understand there are only so much buttons on a controller, but the keyboard is covered in buttons, so you should be able to let me assign these commands as I please. Having sprint, take cover and roll all on the one button is just a pain in the ass. This has been a problem with PC games (mostly PC ports) for eons, just let me change these damn buttons so that when I want to take cover I don't end up rolling against a wall like a bloody idiot.
All the buttons you could ever need, and then another 20 for good measure.
Another problem I have ran into with a few games (again mostly on PC) is really poor control layouts. I want controlling a game to feel like second nature, to be able to focus on what's going on in the game and not have to keep looking at my controller/keyboard trying to figure out how to do something. A big offender of this was ARMA 2, as someone who has played his fair share of shooters; this game confused the hell out of me. I think I spent more time reformatting all the controls than actually playing the game, I swear it is like someone vomited out the control scheme and they just ran with it.
If we wanted to boil this down to its most basic form then, controls get in the way when they aren't intuitive, it is pretty much that simple. When the controls don't make sense or they frustrate you then they are getting in the way and ruining your enjoyment of the game.
So what about motion controls? Right, if we let all those moans die down so I can talk, then I will say that motion controls have a lot of problems with them, the main one being that they don't really work. Motion controls have failed to dominate this generation (apart from the Wii I guess) both the Move and Kinect have been left to die (but they might make a comeback next generation). So can motion controls
become a better way to control a game? The main problem I see is in the whole motion part of motion controls, for starters gamers are really lazy and also moving around isn't easier than just pushing a button, so they would get in the way. I don't want to write motion controls off entirely, as they can work sometimes, but for the majority of gaming I feel that they would be less effective than a simple button based controller.
Having to push 0 to aim? No wonder those ARMA devs were arrested
So when do controllers get in the way? When you are really angry at a game and you want to throw something, then they end up lodged into a nearby wall. Seriously though, the majority of games have decent controls and I feel like for the most part it isn't an issue, but sometimes the control layout makes no sense or can't be changed to your preference (left-handed gamers for example) then it gets in the way and decreases your enjoyment of the game. That of course is the one thing a game should never do, because games are supposed to be all about enjoyment and when you get in the way of that, you have failed your job. Bloody game developers.