The stock Cooper S brakes actually do a pretty good job until you start adding serious horse power.  If you stick with the stock calipers, consider Carbotech pads front and rear (XP10 front and XP8 in the rear.)  Swapping over to the Gen 2 Cooper S stock calipers gets you the same set-up as the Gen 1 JCW brake kit at a much lower cost. Once you add more power, consider a Wilwood BBK.