This is a classic mistake and once again, what's most surprising about it is that games persist in making it. One factor that harms entertainment is that some developers treat mouse and keyboard as secondary setup. The difference between those and gamepads is significant, because usage patterns differ. For instance, keyboard is better suited for 'broad' interfaces, assigning a key to each action, whereas gamepads rely on the 'deep' variety, in this case: button combinations and sequences. Simply mapping buttons onto keys, or vice versa, is often insufficient. But that is exactly what many developers do.
Assassin's Creed Edit
A good example of this is Assassin's Creed. Its controls make a fairly good sense when playing with gamepad, but the keyboard/mouse mapping is unwieldy and counter-intuitive. Even worse, the developer has imposed an artificial, and very severe limit on mouse sensitivity, probably to match it with the maximum turn rate available with gamepad. There is no gameplay reason for this, because instant 180-degrees turns are available anyway, as well as looking behind avatar's back. In other words, higher mouse sensitivity would not give the player any real advantage, other than being able to play comfortably.
Dark Souls Edit
Another good example of this snack is the original Dark Souls. The game is originally released on Playstation. The controls of this game were very fluid and easy to use with a gamepad, which is necessary to play the game. However when the game was ported over to PC, the designer didn't seem to take a lot of time to set up smooth controls. They do not follow a typical control system on PC. What was even worse was that, the on-screen controls were still showed based on gamepad controls. The players can see the controls in the keybindings (which are in the menu), but it is hard to bring up the menu at first place.