I own a PS3 and have plyed countless number of times round my mate's houses and I can play pretty much as well on either of them, obviously owning a PS3 means I am sligtly more used to the PS3 cintrollers. Obviously the biggest difference is the size and the sensitivity of the analouge sticks but you can easily get used to it.
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)