I've run APR on all my VAG cars 1.8T's (Stg1 thru Stg3+), R32's & S3's, and have always been impressed by the OE feel of the delivery and way the extra power is delivered. I know others have had issues with APR but personally I've never had a problem with their software. I have driven plenty of 2.0T FSI cars with their software, and when driving them on the road was that it felt like it improved the K03's more than the K04s. This is a subjective opinion of how the cars felt behind the wheel, not necessarily how they performed on the dyno.
My colours aren't nailed to any particular mast anymore so I'm biding my time before getting the ECU upgrade, but I still have a preference for APR knowing the R&D facility and the quality of the engineers that produce the code. I haven't owned a VW or Audi that ran any other type of software so not able to comment on their day to day driveability. Hope this helps.