The vibrations that you feel are a symptom of pairing the 2.0T with the Tiptronic Automatic Transmission. The 6mt A4's do not have this vibration, and neither do the DSG cars (A3/GTI). It makes the car louder as well. I noticed the loaner A4's (tip) were all the same as well. It is a well known idiosyncracy with the Tip A4's on audiworld/audizine etc.
With that being said, I used to own a 2006 NON S-LINE Quattro 6-speed (jones is a dick lol)
If you can swing the increase in price DO try to find a S-Line. They look much better, more sporty etc. They add bigger door flares at bottom of doors, S4 like front bumper and larger grille, S4 like trunk lid with larger molded lip spoiler, and painted rear lower fascia. It also adds interior bits that I forget, I believe colored stitched steering wheel, s-line kick plates etc.
The 2.0T engine is great in any platform they put it in. As Jones said, great response to mods, xmas sales of APR chips can usually get you a full chip (93 octane file, valet, 100 octane file etc) for around $700. You can also get cheap test pipes on ebay for like $200 and have 300wtq.
I had mine for 24k miles and only had a small coolant leak because of a broken nipple (lol)
Just some random info, an A4 S-line 2.0T Quattro 6 speed won a C&D AWD Sport sedan comparo against Legacy GT, Volvo S4 T5 AWD, Mazdaspeed 6, BMW 330Xi, Lexus IS250 AWD. Even being 1 second + slower than the 2nd place Legacy, it still won.
They are great cars, and as you can tell, I can't say enough about them. haha