I've got a '07 S automatic (R56) that I've owned since new. Got about 60k miles on it now.
The strut tower issue is a known problem on the earlier cars, but was fixed on the R56.
I had a bad dash rattle and a software upgrade fixed under warranty. When I bought my car BMW was offering 36 month free maintenance. I think they have extended that to 60 months. That's a good thing, as any work or parts done on the car are expensive, including oil changes and brake jobs (the latter can be $1000+ for all pads and rotors). Essentially, you've got an economy car that gets fixed at BMW labor and parts prices.
I had to replace the thermostat housing, which I did myself for about $120. Not a particularly easy job, but doable at home if you are used to working on cars and pay attention to all the electrical wiring disconnects you have to do. If MINI does it, it is $500 to $600. This is a known weakness on the car. It is a plastic housing attached to the engine block (how stupid is that). Eventually the heat/cool cycle splits the seam on the housing and you find your coolant on the floor.
The water pump is also a known problem, but MINI has finally been forced to recall the cars for it. It became a safety issue, since an engine fire could result.
There have been lots of reports of timing chain issues. Great if your problem appears during warranty period, but, if not, too bad$$$.
The direct injection causes buildup on the valves and some rough running. This is easily fixed with a Seafoam treatment.
And, yes, the windshields take a beating. I've got the original on mine and it is badly sandblasted and has several bullseyes. It hasn't cracked, though, and I'm loathe to replace it any time soon because I know the next one will take a beating, too.
The runflats are horribly expensive and ride like wooden wagon wheels. I replaced mine with regular tires and I keep a Dynaplug kit and a tiny air compressor in the car. I've had to use them several times. You can buy the space saver spare (included with the non-S cars), but have to store it in the cabin.
Honestly, I love to drive the car. It is great fun and does the scalded ape impression pretty well. However, my commute is about to get much, much longer and more bump and grind and I'm loathe to put a high mileage on the Cooper. I was going to sell it and buy something more bulletproof, like a Mazda3 or Ford Focus, but my wife likes it so much we've decided to keep it for her. She stays at home and just drives to the grocery store and the like. But I get to drive the appliance Toyota Highlander that we got for her a couple of years ago. Somehow I knew I would get stuck driving a friggin' SUV only because I hate them with a passion [sigh].