I received the same advice as you regarding auto trans. The 2.0 FSI with auto box are the most prone to failing, however the 1.6 for some reason were less so.
That being said, like with anything, with proper care and attention it may never be an issue. My folks had one that lasted until about 190,000+ kms before the trans started making funny noises.
My wife had her heart set on one too until she drove an E46 MS with the suede and carbon black interior - we ended up with that ;-)
I do have to buy her a Mk6 GTI one day as payback though!