More and more in recent action games, developers have wanted/tried to implement cover systems to help the player avoid enemy fire. When it works, it can work very well and make the gameplay experience much more enjoyable. When it fails, it can completely break a game and not make it fun at all, frustrate the player and make the game much more difficult than it needs to be.
Let's look at two different games. One that works, and one that tires to, but fails in the process.
Good Idea: Gears of War
This game is a prime example (for me a least) of when bad cover controls make a game more frustrating than it should be. The premise is interesting, the characters have interesting traits, but the cover system simply does not work well. Now while this game isn't built around cover, you do need to take cover in parts of the game to survive. Trying to use cover in this game is like playing rock, paper, scissors. Sometimes it works, sometimes seems to work and sometimes it flat out fails. The controls are frustrating as well. Your character won't always hide behind something, causing you to get shot alot. It doesn't help that the aim is floaty either.
To summarize, utilizing cover can either make or break a game. When implemented well, it can be incredibly satisfying and fun. When it's broken, it can be very frustrating and can take you out of the game. Now I know there are other recent games (Uncharted) that have used similar cover systems, but I haven't played those games and I just wanted to focus on something I had played to give a perspective.