My experience is similar.
I've been driving manual transmission cars since 1988.
I've had 3 VWs and 4 BMWs in that time.
I now have my first Audi (A4, manual tranny). I've had this Audi for 15 months and have driven it 30k miles in that time. In all of the aforementioned cars, I've covered about 250k miles, including about 40k miles auf die Autobahn.
Despite that amt of miles covered, I still don't feel I shift my Audi very well. This is largely because the clutch engages very high. I'm told that the clutches are hydraulic and no adjustment is possible.
Here's a situation where I wish the Audi was more like the VWs, rather than vice versa.
So it really is a case of Übung macht den Meister.
Good luck... to both of us.