Knowledge is power. This forum offers a lot of knowledge which you can use to your advantage if you have problems. But you know when you search on the internet for 'headache', you almost always find 'tumour', or if you watch "air crash investigation" on Discovery you'd believe all planes are going to fall out of the sky ...... well this forum is the same
it encourages you to think the worst ......
Anyway, most R56 problems have been with the Cooper S, not the Cooper, and even the 'old' R53 MINI had its fair share of problems, but both models far fewer than most other manufacturers, and generally good dealer support. If you expect to go to the dealer with 1 or 2 minor faults a year, you'd be right on the average for MINI.
The R56 Cooper is a lovely car - I had one for a time and loved it before changing for a JCW GP. It had a couple of minor niggles (search if you like as I reported them at the time) which the dealer sorted out easily enough.
So, you certainly haven't made a mistake. I would ask why you didn't go for the Cooper D, but that's about all I would question - enjoy your new car and don't forget to post some photographs !