I'm up to Chapter 8, and the only annoying thing so far is that you can't open a door while dragging a body as it uses the same key for both.

So, you have to drop the body a distance from the door, then open it, or open it before-hand.

Also, like Bioshock 2, it doesn't display on-screen prompts for mouse side-buttons, so it says Press to enter cover.

The controls are generally done well, though, and it's great that it changes from keyboard to controller prompts depending on what you're using.