Yeah, my bro had a manual..but I drove automatics too, because at one moment my Dad was thinking to an e46 too. And he only drives auto. So it's not the gearbox, even if I found Benz gearbox better suited to the engine. The Beemer changed gears too high, let some little feeling of the gearchange sometimes...not as impressive as Benzes' tranny.
I drove the A6 2,7tdi auto, too. Impressive, of course, but did not really convince me... Somehow it dod not felt as... impressive as 30d or 320cdi. Powerful, silent, but it did not felt as..you know, as perfect, as torquey, as easy as the two others.
My bro also had an A4 with the 2.5tdi 150cv

...What a noise! really pleasant noise. But too noisy, too slow, and of course turbo/debitmeter went broken...
The best noise ever for a diesel was the old W124 300 turbo 143hp...That sounded better than a 300E

The 525tds sounded good too!
No diesel can match these old units for the noise.