Problem with the dual shock is that it was basically an extension of the super nes controller which worked for the PS1 but was outdated for their second and certainly their third console (e.g. the emphasis on the d-pad was redundant once everything went 3d). They never really addressed it and kept shoddy analogue sticks and an uncomfortable form factor for two whole generations.
My personal favourite controller is the wiimote+analogue. It's miles better than anything in terms of comfort and use, but obviously it lacks the quantity of buttons for some specific games. When done properly, however, it was far and away the best control method ever seen on a console.