undoubtabley the xbox has the better controller layout and its a fact and i mean fact. You can get used to both of them but xbox will always feel more natural. I have never owned a xbox and played playstation consoles my whole life (im no fanboy so shut it if you are) and im used to my ps controller and good but when i pick up a xbox controller it just feels right. Even game companys prefer a 360 controller. (orginal xbox controller sucked just cuz of the white and black buttons positioned awkwardly)
i dont really think it feels more natural it feels weird at first and its easier more natural to move thumbs forward to dpad on ps3 than backwards on xbox
I like the xbox controller layout more but I know a lot of people who have replaced their control sticks with those of a playstation because its more comfortable and offers you more sensitivity/control which will give you more precision, having tried an xbox controller with the playstation sticks I can honestly say that's the way to go.