I'd say it depends how critically you listen to music. The stock system is pretty good. If you listen to your car radio mostly as background music or talk radio, and generally listen to music at home the same way, you will find the stock system more than adequate.
If you're the type that sits at home with a cocktail in front of your stereo/home theater system closely listening to music with the volume up a bit, or are a musician and appreciates the tight bass, transparant highs, and the extra harmonic detail that the h/k system provides, you will regret not getting the L7 system.
Aftermarket systems many times distort the asthetic layout of the car (who wants a stupid looking aftermarket Sirius tuner screwed into the dash of their new E90, for example), are generally more unreliable, and you always run the risk of a botched installation job by some mom and pop stereo shop.
Inclusion of the L7 system is one of the reasons I stepped myself up to a 330i. Strangely enough, it is an option on the more expensive 525!! Of course I am a bit biased as in a former life I was a h/k manufacturers rep.