You can't up a speed manually in AT to lessen wheelspin on exits, nor use engine braking with AT to slow down where you'd prefer not use brakes.
All in all it allows (IMHO) to maintain the car in good "tension" while with AT you rely on the gearbox to react, meaning you have to slow more so the gear shift down.
And if you want to fuel save, you can upshift earlier, while in AT...
I don't think AT operates in a range as good as the MT can be.
I remember some time ago in a online time trial at Red Bull Ring with an Evo IX, that exiting T3 (the 90º right hander up the hill) in 3rd worked wonders while leaving that corner in 2nd costed me 0.3 in the middle sector alone.
It sure felt more natural using the 2nd, but the car had a nice power band and then the 3rd were better estability and turbo lag wise.
Another day we had the Nissan GT R35 at Nurburgring sprint. Braking into the 1st corner we had to use braking engine, by timing the downshifts we could stop the car in a better way.
In the current time trial with the BMW Z4, there are occasions we shift up to 4th mid corner in order to provoke more turning in.
That's just examples of how using MT can be way better. I picked up hese things from the time trial thread and they helped me getting gold at said events.
