i had 3.0 quattro and loved it. It was thirsty and they are no way near as tuneable as the 1.8t but in my opinion drive nicer and the soundtrack was great (particularly through a milltek) i would say there are far less potential problems as well. i wasnt looking for any specific model when i brought mine i just wanted a quatt sport 1.8t/2.5tdi/3.0 or an s line 190 and tried them all however when i stummbled across the 3.0 i had to have it.
I had a similar choice to make when I decided I wanted a performance 4WD Audi A3 variant.
It had to be 4WD and plenty of performance and equipment/luxury. I excluded the V6 Quattro due to my worries about tuneability (should I want to tune the car), the heavier front end which normally means a tendancy to understeer and very many reviews which, amongst other things, suggested the S3 chassis is better sorted. I also had previous experience of both V6 and Turbo engines and have to say I always feel more engaged driving a Turbocharged car. Potentially higher tax and running costs had a small influence too. Manual was also a must but I didn't get to the stage where I looked to see if the V6 Quattro did a manual version over the DSG.
I don't doubt the V6 quattro is a great car but the above were my reasons for chosing a modified 2003 Facelift S3 and I am very happy with it
BTW I even get averages of 34 mpg and generally higher if I do more frequent fuel computer resets and that's without pussy footing around !