7500 miles on my '04 and I experienced the same thing. 100% agree with kuhlka on the oil changes - have done three since I purchased her and it seems to make a difference. Once the oil starts to break down, the tranny gets a littler more "clunky". Also, the "blipping" the throttle prior to shifting into first is something I have done on all my bikes and it does seem to make a difference on my S3.
As for false neutrals, I have not experienced but 1 or 2 to date (probably rider error anyways) and it does not seem to be an issue on my S3.
Basically, from my experience thus far with my S3 and all of the posts I have read on this subject, what you are experiencing is quite normal.
I have learned to ignore the tranny, chalk it up to that is how it is, and just enjoy the ride - I still have a grin every time I hit the throttle - and I ride pretty much on a daily basis..........