The first thing that comes to mind is Mass Effect 2, changes made to combat system rendered it tedious, disappointing and overall boring. Biotics are pretty much useless (shielded or armored targets being immune to them is just bollocks), ammo system that makes no sense (all guns use the same clips, but they aren't interchangeable between weapons), the whole gameplay essentially being Tour de Chest-high-wall... fuck that.
The second one that stands out for me is Broken Sword 3: The Sleeping Dragon. A sequel to two point-and-click adventures, which doesn't utilise mouse on PC. If there ever was a shining example of horrid consolitis, it's this. Four directional keys for movement, four others for interaction. No accuracy whatsoever. The game itself isn't bad, but the controls are doing their best to kill the experience for you.