I think the crux of this issue is perception.
Although it is possible that main dealers are as good as independents, I don't meet many people that think that way and I certainly don't.
There are a couple of issues involved: setting up an independent specialist, like Jamie has with the Alfa Workshop, tells a customer that he is passionate about the marque and wants to work with it. This might also be the case with a main dealer but it's "hidden" behind the corporate involvement. For the record, I was really pleased with the work done at the Alfa Workshop, but have also received great service from a main Fiat dealer locally.
Then there's the issue of workmanship, irrespective of passion. If an independent keeps on doing poor work, their reputation suffers directly. Again, the main dealer has a "cushioning effect" because the perception is clouded by the overall marque perception.
I also find independents to be more direct, and less interested in selling related services etc.
I do accept, however, that there are good and bad on both sides. The key is to find someone you trust and like, and for now, the main dealers need to work on their reputation generally.