I've owned both...
Depends on what you want, the Cooper S has more... OOOMPH! If you want something you can drive feeling like a maniac but being very safe then the Cooper S is great and def worth the extra over the Cooper, if on the other hand you're just popping to the shops and are happy with a softer ride the Cooper will do but you may even want to consider the Mini One. Whichever you get make sure it has the Chili Pack otherwise the car will depreciate a lot faster. If you do a lot of motorway miles you may wat to consider the S, t is more responsive when accelerating than the Cooper allowing you to get out of the way, or overtake, quicker.
Take them both for a test drive, drive them how you would normally and see which you prefer.
Oh andone last thing, whicever you decide on, ENJOY IT, Mini's are soooooo much fun!