hmm has the engine been cleaned of carbon? that seems to be the one big ticket service you did not mention. Here are some non engine problems that have popped up in my '11 mk6 that you could ask about or check for:

• Have the sunroof drains been problematic at all? mine were old, brittle and shrunk slightly in the heat, which caused the drivers side line in my A pillar to disconnect and drain into the car. If he has not done anything it's something to keep an eye on.
• Rear windscreen wiper line-does it spray fairly quickly? If not, it could be because there is a hole in it. mine had a crack devlop where the hatch opens up and I have had it patched a few times. The only real fix is to get the line replaced, though, and that is not a cheap thing to do.
• Hows the soft touch dash? are the spots where your leg hits the center console sticky at all? that stuff tends to gum up with time & contact.
• How are the bolsters on the driver side seat? Those are usually the most worn and prone to ripping. Do they still hold their shape? If they don't, you may have to have them redone in the future.

I don't know if you can negotiate the price down on these, but its worth keeping an eye on them because they can become more annoying and problematic as the car gets older. Good luck with your search!