I feel that using the mouse and keyboard is better than a controller, but that's just me. I can use both dual analog (PS3 or 360) too, but a lot of times I kind of wish that I was using a keyboard and mouse when I'm playing a console shooter.
Sometimes it just depends on the game though. Killzone 2, for example, felt great on a controller while other titles like Resistance 1/2 (multiplayer) and Call of Duty 4, World at War, and Modern Warfare 2 are ones that I hardly care to play with a controller. After playing The Orange Box and Left4Dead on consoles versus the PC, I hardly want to touch the console version.
One argument that I see some people make about the dual analog sticks is the movement. I just don't get the argument since I don't think being able to slightly tilt the stick really matters (certain exceptions apply) and I've had plenty of falling deaths from fudged movement in both PC and console titles. Not only that, but I'll flick the analog stick in a direction multiple times to position myself better just like I would tap the keyboard keys to do the same task. If I really need it, there's usually a walk button. Otherwise, crouching and moving works just fine. Heck, I didn't have much of a problem using my mouse and keyboard in a third person action game with a revolving camera (where you don't control like a tank) such as the Arkham Asylum demo.
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