Cover systems are typically met with mixed responses. The video games industry seems to love them, while audiences meet them with mixed feelings. Chances are if you've played an action game lately, you'll have played one where there's a context sensitive button to hide behind some object. A lot of people seem to find it frustrating, asking whether it was worth having in the first place. I personally think so, and to see why, we need to take a broader look!
The first shooter I know of which gave the player this type of cover mechanic is a game called Kill Switch from Namco, released in late 2003 or early 2004 depending on the region and platform in question. It was perfectly comprehensive. The context sensitive controls enabled you to quickly cross gaps between cover, and also blindfire. It's reception was mixed, as it's ratings on Metacritic range from 75 to 66, and in this day and age, it seems to have been mostly forgotten about. The developers of Uncharted and Gears of War credit it for their inspiration though. In fact, the lead designer on Kill Switch, Chris Esaki, has been helping out with the development of Gears of War for quite some time now.
Kill Switch is the first time this type of control scheme was present in a shooter, but fans of stealth games will be familiar with it from even earlier. As Metal Gear Solid has implemented a similar control scheme since day one, which resided on the PS1. More recently, it's been present in every Splinter Cell game and was introduced in Thief 3 too. Or alternatively, if you're into arcade shooters, it could well be reminiscent of games like Time Crisis, which let you dive in and out of cover at will.
Going back to it's presence in shooters, these types of context sensitive cover mechanics have had a place in AI for NPCs for quite some time. Half-Life 2 demos from 2003 show this in action, as NPCs can be seen using cars and rubble as cover. However something which can lead to frustrating deaths and easy kills in modern examples is where the 'cover' button doesn't properly cover you. If anyone had the patience to play Kane & Lynch 2, they'll have no doubt found themselves getting hit despite being as concealed as the game will allow. And by the same token, there will be enemies you can shoot who simply won't react before they drop dead. As their AI tells them they're in cover, forgetting about that small piece of their body which you can see and shoot.
This type of control mechanic has been criticized a lot. Especially by the Escapist's Yahtzee in his Zero Punctuation videos. The makers of Deus Ex: Human Revolution seemed to realize this, but felt they couldn't be without it. It's a great tool for stealth strategies, which was going to be important. But alongside it, they had to include functional gun play too. So what you're left with is a game which accommodates both. The cover system still lets you aim, shoot, and blindfire if you use it in a fight. Or alternatively, you can simply peek out if you're going for a stealthy approach instead.
If you want to, I gather you can play the game without ever using it's cover system. Though I personally won't be trying it, I find it too useful. But it's a nice example of it being well implemented I think.