Driver's console.
Door fit.
Many electrical problems.
Cambelt tensioner (twice involving two top end rebuilds).
And many more minor problems.
Poor response from dealership to problems. Took part in an invited Audi customer survey - 10 people invited at random, 8 of us had major problems!!!
I have not found the problems you encountered. I have a 97 A6 2.5tdi old shape with 180,000 miles and still original gearbox, clutch, drives. The only things changed are cam belt fuel pump belt tensioner, water pump, disks, pads and drive boots. Apart from that regular oil and filter changes with semi synthetic oil.
The only breakdown was the flywheel started to become loose (it has a rubber shock absorbing middle) and this started rattling. I never use Audi main dealers as they are rip off prices.