It all depends on what you want to do and why you think the current audio system is lacking...
In my experience in my Leon with the standard sound system, I find the midbass response is fantastic, the midrange is very poor and the tweeters are poor. Its a typical OEM sound but for everyday listen to the radio etc, its just fine.
I, like yourself, also experience the ratting door cards at reasonable volume, there is a free cure - turn the bass down on the headunit, or the more expensive option, but the proper way of doing it, is to deaden the door card as mentioned already and then use a layer of Silent Coat Sound Absorber 15mm and line the inside of the card...this will eliminate all rattles
I will be taking a much more indepth approach to the sound system than most when the time does come to upgrading. Either 6x9 or 8inch midbass drivers in the doors, 3inch full range drivers in the a-pillars, not sure about what to put in the boot yet!
