I have an 06 MCS with 84,000 miles on it.
Prior owner had the water pump replaced at 70,000 miles, a month before I picked it up.
Only thing I had to replace was the upper motor mount $75
Weak spots for the R53 models are:
Power Steering Fan can fail-overheating the power steering motor
Leaking Power Steering Hoses
Front Lower Control Arms bushings are usually toast by 80,000 miles
Super Charger life span for the 05 and 06 is a bit more then 100,000 miles, replacement is only $1,500 and will outlast the car.
Strut Towers Mushrooming
Passenger Seat airbag sensor issue ($1,100 part)-can be bypassed
Check for rust in the rear hatch by the battery and the door sills under the gasket
Ditch the run-flat tires-use AAA
No timing belt to worry about.
Other than that I love driving the "Go-Kart" feel
Wayne has a list of Tech articles
Pelican Parts - MINI Cooper Technical Articles