The CVT automatics on the firs-gen r53 Minis are shit. Get a manual or the automanual in the second-gen r56.
Because dealers strongly recommend prolonged oil service intervals on brand new motors, many 30-40k mile Minis have only had 2 oil changes. Unacceptable especially on high-tolerance forced induction motors.
The short wheelbase makes for a jarring ride. Handling is superb but a comfortable highway cruiser the Mini is not. Factory 16s ride kind of harsh, 17s are nearly brutal, God have mercy on you if you go 18s or up. This coming from someone who rides 19s on his 90s Toyota. Replace factory run-flats with a quality tire asap.
Fuel economy is excellent even when driven spiritedly, even a FI model.
The leatherette interiors aren't easy to maintain and show their age quickly. Go with real leather interior if possible.
Panoramic sunroof, multitouch steering wheel, heated seats/mirrors, xenons are some of the more important & desirable options.
JCW editions are SWEET! I've seen many sell at very tempting prices. I'd be looking exclusively at them if I was back in the market.
Try to find one from an enthusiast owner who can provide proof of unscheduled maintenance. Not an easy task given most are driven/owned/leased by people who could hardly care less about such things.
r53 vs. r56 is usually a pretty heated debate. I like the styling & added size of the r56, and the fact that the S model is turbocharged in the r56 vs. supercharged in the r53.