I have had 2 6 spd MKIVs and I know have an automatic.
I'll try to answer each of your questions:
Acceleration: ATs seem to be quicker in the 1/4 mile because they are more consistent and easier to get low times. The AT also has a good pull in first gear and in second gear. They are both pretty tall gears but the pull is pretty strong so it feels pretty fast. It seems to me like the turbos take longer to come online in the automatic however. Thus, the initial throttle response is slower in an automatic but once it starts boosting it feels faster.
Top Speed: I don't know. I have never gone over 150 in any of my cars.
Trading off power for convenience: I don't really know of anybody who buys an automatic for convenience. Usually, people buy the automatic because they cannot find a good deal on a 6 spd. Some also buy it because you can usually turn better times in the 1/4 without a single. Generally speaking however, there is not much of a trade off of power for convenience(you have more parasitic drivetrain loss due to the automatic). It is really a matter of the usability of the power. Many people find that the automatics are more boring than 6 spds.
How much power can the auto take? The auto seems to be able to take BPU++ without too many problems. I have been told that you can go to a small single(sp57,t60,t61) without blowing it up which translates to 475 - 500 RWHP.
Adam