In my experience the independents are better at locating problems and issues and thats were I'll be heading when my car is out of warranty (which is soon) for all future work on the Mk5!!
I agree that independents are generally better at locating faults and problems etc. However, they do still need to be a VAG specialist independent, and have the correct diagnostic equipment.
One of my mates is a very trustworthy independent, and whilst he isn't a dedicated VAG specialist, he does work on a lot of VAGs, and is a bit of a Corrado fan. He has some very expensive SnapOn, and SykesPikavant fault code readers, which both have the extra VAG add-on modules, but they are both useless when compared to the genuine VAS5052, and the VAG-COM.
Neither machine could interrogate a number of modules on my B6 S4, and on the few modules they could interrogate, they both gave incorrect readings on the ABS module. Fortunately, he is very trustworthy, and reliable, and I know he wouldn't rely on faulty or wrong readings.
Unfortunately, there are many out there that are simply out of their depths with modern CAN-BUS electronic control module diagnosis.