While aiming is better with a mouse you don't ever hear about movement being better on a controller. Obviously it's not as important but a joystick in terms of movement is far better than a key.
I agree but it depends on the game's needs. The joystick's advantage is that it can be progressive. Can be useful in game where your movement speed have to be controlled more precisely, like a action-platform game (a la Tomb raider or Assassin's creed for example).
For a FPS ? Im not sure, unless if it's a RPG or infiltration game with FPS pov. Precise aiming of the mouse is more important for me than being able to have a smooth transition between run, walk fast, walk...
Now imagine a new peripheral that could combine the 2 ?
@Shawodcat : are you sure they are just beginning ? I have had these bunch of thrustmaster pads for some time now, for my PC, and they have the dual anolog sticks, along with pad and the whole bunch of buttons, enough to provide for xbox ports and all... But it's true that appart from multi platform games and ports, there aren't many games that exploit the pad to the max, I suppose. Still, more than console games using mouse and keyboard. Each have their standards