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Mine are factory front and rear and I like them. I have stock sized 16" tires and it does seem to protect the car a bit better. We haven't had much bad weather since we got the cars so the jury is still out in my opinion.
My previous R56 had factory front and back and I would say they did help on those cars.
I've got the factory ones. I purchased them after I got the car and had a local MINI specialist install them at my break in oil change. They're great. And I think they do their job pretty well. I've got a black car, so the mudflats aren't all that noticeable.
Just read this thread the other day, and it reminded me to buy the mud flaps for my new Mini. I had them on my previous two Minis, but neglected to order them for my new one. I've had the car for a month, and last week I had to drive (slowly) over some lose stones and I could hear them hitting the underside of the car as they came off the tires. I've now ordered the mud flaps through my dealer and will have them installed shortly.
I've installed a couple sets and they are really easy to install. We do recommend NOT having any dressing on the arches. The tape will stick better from the mud flaps if they are dry.
The Front ones work well to keep dirt off the side of the car http://www.waymotorworks.com/mud-fla...i-hardtop.html
The Rears not sure how much the help, but they can't hurt with how dirty the boot gets.