I also have a 2007 MCS with HIFI.
I started by replacing the speakers with Infinity Kappas and Dynamat. I did a
rear-seat-delete, so considerable soundproofing was called for.
I learned later that this was over-kill with Dynamat. It stops a panel from vibrating, but doesn't block much sound. So, you don't need to cover every inch. More about soundproofing later.
The Kappas improved the clarity considerably over stock speakers. However, the sound was too "bright" for my taste. Polk speakers might have been more to my taste, but I went nuts and decided to put in an amp.
Now I'm in the middle of a DIY install of an amp and higher grade speakers (all from
Image Dynamics). The HIFI system cuts off bass to the rear speakers and puts it all in the lower speaker of the door. This is a fairly small speaker for handling the bass. One advantage of having the HIFI option is that the signal at the X9331 connector under the dash does not have this off filtration. So, it is easy to pick up a full range signal to run a powered sub, or an amp.
I was running a Bass600 8" powered sub ($130 or less at Amazon) with the Kappas and it helped fill in the bass missing from the rear 6x9 speakers.
I've also learned more about soundproofing and will be doing some additional work on that. I found this site useful for soundproofing material:
Sound Deadener Showdown
Since access to the doors is difficult, I'm using this:
Dynamat DynaXorb Speaker Kit
If you remove the battery in the MINI you will see a big port for the fresh air filter. I read somewhere that this was designed to let a certain amount of engine noise into the cabin for a "sporty" feel. Unfortunately, it also lets in significant road/tire noise. I'm going to attemp to reduce this noise by applying a mass loaded viny & closed cel foam barrier (MLV/CCF) to the plastic wall between the fresh air intake area (houses the battery and windshield wipers) and the engine bay. I'm hopeful, but not certain this will help.
Tthe wheel wells seem to be one of the significant areas to deal with. I've put Dynamat there, but may add some MLV later. There is a thread here about putting Dynamat in the wheel wells.
Another thing that helped was creating mats of MLV that go under the floor mats. I made mine extend beyond the floor mats to cover some of the firewall, and go under the front seats (from rear mats).
MLV is heavy stuff (that's why it stops sound) so you will be adding weight to the car. Dynamat is also heavy, but much thinner. Dynamat stops a panel from ringing, but it doesn't block much sound. Several sites recommend Dynamat (or equivalent) topped with CCF and then MLV. The CCF isolates the MLV from the panel. The MLV absorbs much of the energy from the sound waves.
I know someone who paid $3,000 for amp, JL speakers, Dynamat, and (I think) a sub. Dynamat is what most places do for soundproofing. It helps, but I don't think it is really enough.