Gamepads sacrifice a little precision for comfort and ease of use; in a game like 'Dark Souls', there are numerous buttons that can easily be mapped to a gamepad, but the keyboard and mouse controls feel more clunky and tacked-on, like they weren't expecting to create a PC port of the game and just hoped we'd plug in the well-worn Xbox 360 controller and use that. They were right - I started it with keyboard & mouse, but changed after about 45 seconds.
First person shooters require quick reflexes, precision, and rapidly spinning around to look for enemy movement and react accordingly; you can't do that as effectively with a controller, especially because the thumb-stick has to lose some precision and sensitivity. The thumb-stick can only move, at most, a couple of centimetres in either direction, whereas the mouse has several inches of mouse-pad to work with.
They each have their function. Really, it's quite a boon to live in an age where gaming hardware is so varied, and USB devices can easily be plugged in to work quite quickly. I remember a time before the Xbox 360 controller, when proprietary devices (particularly steering wheels) were apt to just not work with Windows 98, or only parts of them would work, ruining the experience as their buttons remained just for show.
Then again, I wasn't as tech. literate back in those days, but hunting around for drivers and solving such issues now seems (almost) a thing of the past, at least if you're not using incredibly exotic or under-supported hardware.