Manual or Automatic?

Don't think that manuals are cheaper. Clutches are expensive, and they wear out (unlike torque converters). And on C5's, they're a PITA to replace.
No TM is a plus tho.
-A
You dont have to buy an expensive torque converter but u do have to buy an expensive cluth/flywheel. It depends on what u want the car for ,i guess.
GOOD LUCK WITH UR CHOICE!
M6= higher trap speed, more power to the ground, more fun to drive(opinion), stronger from a roll
A4= better in traffic, torque multiplication, and with a TC nasty from a dig.
Good luck,
Mike
When I lived in Chicago the A4 was great in traffic, kicked butt stoplight to stoplight and was awesome in the 1/4 mile BUT nothing can be more boring then an A4 car around here on a 1/8 mile dragstrip.
Putting a torque converter in an A4 vette is almost as much of a pain as the clutch, done both several times. The syncros (different design then the f-bodies) in the M6 vettes seem to hold up better then F-bodies but the clutches in the 97-00s are just as crappy as f-bodies. They last if they arent beat though..
I miss an auto at the dragstrip but I went with an M6 in this car, have a lot more fun with it but the trans is out of it getting rebuilt
Thought a few times about switching to an auto but I am having too much fun (costly fun but fun) to put an auto in.. 
