I am working on my 2006 Mini S order and have been struggling with the audio part of the car. After talking to tons of people here is the best solution I have found:

What I want is:

Sirius Satelite radio
cd player with MP3 capability
an Ipod adapter
and a top notch sound system

Prefer stock look but I can't get what I want!

I have removed another system from my old car that I am going to re-install to meet my needs and use the factory steering wheel controls:

I have an Alpine CDA 9835, Alpine Ipod adapter KCS 420-i, and Alpine Sirius receiver module.

As I said ...First of all I wanted to go with a factory Mini solution but I can't get what I want with their system. So I went to some guys I have endorsed since 1976...Crutchfield.com I bought my first Pioneer Supertuner from them back then - from the man who started the company in his basement...Bill...and they are still among the best with their tech support and prices today.

Here is the solution:

Don't order navigation
Don't order the HK speaker system - it has a factory amp and you will not be able to use the factory speaker wires.

Using my Alpine CDA 9835 , KCA - 420 I and the satelite receiver I can have Boston Acoustics speakers and a sub under the seat. Add the factory steering wheel input and I can see all my ipod tracks and sat radio on the display. Any item that the remote will control can be learned into the steering wheel control. This should rock. If anyone has other suggestions I am open to them. The rear speakers have free brackets for a 6.5 speaker into a 6 X 9 opening. They will act as mid-ranges with the sub kicking the bottom end. All of these items are plug in with no cutting and the items include installation in the local area.

And here are the products we discussed:
065S65RC Boston Acoustics S65RC 6-1/2" 2-way Speakers Shallow Mount
065S65RC Boston Acoustics S65RC 6-1/2" 2-way Speakers Shallow Mount
120999302 Mini-Cooper 2002-Up Kit/S/E
120709003 Volkswagen Wire Harness
12040EU55 Euro Antenna Adapter OEM F to Motorola M
127SWIX PAC SWI-X Steering Wheel Radio Control Interface
597421002 InstallCard: Speakers or Sub (Prepaid install - 1 spkr set or 1 sub)
597421000 InstallCard: In-dash Receiver (Prepaid in-dash receiver installation)
113KSCSW1 Kenwood KSC-SW1 150W Compact Powered Subwoofer
597421006 InstallCard: FM-mod Satellite (Prepaid FM mod/direct connect install)
597421003 InstallCard: Amp or Equalizer (Prepaid amplifier or EQ installation)
127BB150A2 PAC BB-150A2 Bass Blockers 1 pair with Terminals, 150hz/4ohm