Having a manual Aero S3 and having driven Aero 8 S4 Auto and Supersports Auto, I must be the only person who doesn't think the Auto box is that good.
On full bore and normal pootling it's ok, but it does still 'wind up' to get going, often seems to be in the wrong gear or kicking down too much, and I can't get used to the forward/back BMW down/up shift since I have had other cars (Smart, VW Scirocco and Subaru Outback) that all work exactly the other way round.
It also dilutes the special experience and that great feeling when you get a gearchange just right in a manual. I really like the clutch in the manual, although the manual box is quite heavy and slow, especially 1st to 2nd and 5th to 6th (on mine).
So they both have their little ways. For a Plus 8 for me, it would have to be the manual box for these reasons and many of the reasons above.
My Scirocco DSG gearbox is mostly a much better auto box and has the paddle shifts as well as the +/- shift on the stick and is the sort of gearbox I might consider as a manual alternative.
