We both own 07's. I had my stereo upgraded by a large high-end shop in Glenview, IL called Abt Electronics -- who are real pros with lots of experience with Minis (and lots of other cars).
At first, I had your stereo question. However, they told me that they could not change the head unit (the in-dash part with the controls and orange lights) because it was an integral part of the Mini's electronics system which helps operate the whole car.
Consequently, they upgraded all the parts of the stereo that are hooked up to the head unit. You cannot tell any work was done -- until you listen to how it sounds--enormously better sound. All the orange read-outs and radio/dash controls look and operate exactly the same as in an unmodified, stock Mini which is kind of cool.
Abt replaced the front and rear speakers, added a removeable subwoofer in the rear luggage area (the only mod you can see), and put in an amplifier under the driver's seat. They also sound proofed the body using a material called Dynamat which makes my Mini much quieter--very good stuff.
This process required taking much of the interior out of the car (especially the area behind the front seats), installing the equipment along with reams of custom wiring, and then putting the back seat and all all the interior panels, etc back in place without a trace. Not cheap, but really excellent work taking a very experienced crew most of a day to complete who had all the needed tools, parts, connectors, etc immediately at hand all the time.
I stood next to the car and watched it all. You'll see posts from guys talking about this sort of work as a do it yourself project--which strikes me as very naive unless your day job happens to be high-end car stereo work.
My suggestion is that you ask around and find the pros in your area, and talk to them. I'm sure Abt would chat with you if you called them. They're on the internet. If you don't want a full redo, talk to the shops about incremental steps.
Hope this helped. Sorry it's so long-winded. Let me know if you have any questions. Happy motoring.
Upgrades
