I have been looking to upgrade my stock (non-HD) stereo in my '07 MC vert (non-S). I have the steering wheel controls and so upgrading the head unit would have been very expensive. My major concern was that the bass response was pretty terrible. I opted to put a pair of kicker 6" speakers in the rear and it makes a heck of difference. The speakers cost $100 + installation. A worthwhile investment!
The Mini stock speakers are paper crap! (see below)
BTW, does anyone how big a difference replacing the fronts would be on the factory head unit?

 

IMO replacing speakers is the first thing you should do for better audio in any car. If you still think something's lacking, then you can think about aftermarket head units with decent amplification built in, or a real amp.