Honestly, as weird as it may seem, a finely tuned automatic tranmission will always be better than a comparable manual transmission (relatively).
Once you get really into making a transmission for performance, you would modify an automatic with a manual valve body and some serious servos. Essentially with a manual valve body shift kit, you are shifting yourself just like in a manual (there is not "Drive" option in a full manual valve body) but what makes the automatic with a manual valve body better than the actual standard transmission is that the cluthing is entirely mechanical and controlled by hydraulic pressure. In a manual, you control the clutching, which leaves room for variables, inconsitancies, and lots of human error. With an automatic with a nice shift kit installed, the changing of the gears will ALWAYS be a hard, fast, and instant exchange of gears using lots of fluid pressure. It's a battle of means to an end, though, because you lose a lot more power though an automatic transmission versus a manual transmission.
all I know is, I can't wait till I finally have my hands on a nice 4L80E and get it all beefed up with the right hardware.