FYI - I bought an '06 R53 S hatchback with the 6 speed manual transmission just 12 months ago. Like you, I had worries about whether it would be reliable and robust given it had the factory fitted JCW
210HP kit already on it.
It had 120,000klm on the speedo when I bought it but was in immaculate condition otherwise. So I took the chance and bought it.
Love it. My friends love it. My family love it. The whine of that supercharger when you gas it is just awesome. I often say to my friends that driving it is the most fun you can have with your clothes still on! ;-)
Adding something like the JCW
210 HP kit makes a big difference to the stock S in terms of acceleration, but there are plenty of aftermarket options for an R53 available if you want more oomph that will probably cost you less.
We've got 2 other stock R53's in the family (an 02 S and an 04 S) and they are also great fun to drive.
I can't comment about whether you should go for the later series Mini with the Turbo or not - I will leave that for other members who have one to comment on their experiences.
1) Would strongly suggest if you're wanting an R53 to try to find a good example with a well documented service history. Ask to see the service history documents and see what has been changed, how often and what other repairs has been done to the car. Unless you're a mechanic yourself, I wouldn't touch any Mini R53 or R56 that has little or no service history no matter what the current owner or saleman says.
2) Listen very carefully to the engine as you test drive the car. Get to know how the engine "should" sound and compare carefully.
3) Look at the colour of the engine oil on the dipstick. If its thick & black, then that engine's not had much love. Remove the oil filler cap on the crankcase and look at the underside of the cap. Peer inside the engine top cover whilst you've got the cap off - look for sludge or deposits of black oily buildup. It should look fairly clean inside.
4) Check underneath for oil leaks as the R53 engine is notorious for leaking crank seals around the flywheel area which can be a real pain in the wallet to fix.
5) Suggest take a friend with you to act as a second pair of ears & eyes. You might miss something whilst you're in deep conversation with the owner or salesman. It can often be good to double-check what you think you saw / or what you think you heard with your friend over a coffee afterwards.
6) Look at the tread-wear pattern on the front tyres (run your hand over the tread surface and feel for sharp edges) and look at the inside and outside edges of the tread. The wear pattern can give you an indication of how the car has been generally driven.
Otherwise, from what I've read the R53 engine is pretty bullet-proof and should be capable of doing high miles if its not been abused and kept well serviced.
Good luck with your search. :-)