This is a popular discussion point, if you do a search through previous posts you will find lots of opinions.
However, thats all they are opinions !
I had this dilemma, but went for the Harmon Kardon. Im happy.
Would I have got a better sound quality with a different head unit and speakers ? Probably, but I'm still happy. Is anyone going to nick the standard head unit ? Doubt it very much.
Best advice I can give is go sit in a Mini with Harmon Kardon, take a few CD's and see what you both think.
Its painfull sitting on this fence...