Personally I think it's unfair to compare mice and keyboards with controllers, and I don't understand why some people like to bitch about how one peripheral is superior to the other. It's as MeechMunchie said on the Portal thread - It's like comparing colours. Both do the same thing, they just do it differently.
Some games work better with controllers because that's what they're designed for (the PC ports of the old GTA III era games are an example of this, also try playing SNES and N64 games on an emulator with a keyboard - It's a little awkward and takes getting used to), other games work better with a mouse and keyboard. I'd like to see someone try and play World of Warcraft, or any isometric RTS effectively with a game controller, for example. There's also a lot of personal preference involved as well.
Here's a good example of game design differences: When I played Half-Life on the PS2, I found it awkward, since Half-Life was originally a PC game and wasn't originally designed to be played with a controller. I got as far as the last level before I needed to turn auto-aim on. On the other hand, Stranger is a game that I find a little awkward to play on the PC even though it's a 3D shooter as well, simply because it was designed to be played with an X-Box controller (even if targeting things in first person mode is a lot easier with a mouse).
I think it's quite a feat to design a game that feels natural and easy to play by using any type of controller - Beyond Good and Evil is one of the few games I think think of that is like this, and perhaps because it was designed to be cross-platform.
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