The choice is simple dependent on what you want.
The R53
MCS had a cuter face, sublime handling, and the engine had plenty of character. However poor fuel economy and high CO2 emissions make it more expensive to run. Buy if you like driving but don't do too many miles. It will definitely put a big grin on your face. It is a car for enthusiasts.
The R56
MCS is a much more refined car, with a great ride and a sophisticated engine. This means plenty of torque, great fuel economy, and low CO2 emissions making it fast and cheap to run, but perhaps lacking slightly in character. Buy if you like driving but do lots of miles. It will still put on a big grin on your face. It is like a MINI grand tourer!