I chose a manual because I think the Tremec 3650 is a better transmission than the 5R55E auto. Now if Ford would have kept the 4R70W in the Mustang, I may have chosen that. I don't feel like trying to swap that in.
I've driven 2 autos and they were fantastic. I could really see being happy with one, though I've heard that they may not hold up in higher performance applications. Still a great drive though.
I had to get the manual simply because, on those rare occasions where I really get to drive the hell out of it, it's that much more fun.
I might have been the first person to say it here, but I am not the first to say it. I have heard that the 5R55E will not stand up to a good high stall TC, performance tune and steeper gears and that came from a pretty good source. I also heard of 2 4R70W swapped 05 GT's. I haven't actually verified what I heard on the 4R70W swapped cars or not.
No matter how good a manual gearbox is YOU will still have to change gear.
And no matter how good/smooth an auto gearbox is, it will never give you the CONTROL of a manual gearbox.
As for performance, well its an old argument BUT by the very nature of design and PHYSICS the manual car will be faster. The fact that not everone can drive to that standard is not a fault of the gearbox.
And before its gets into the hows and the whys and who runs what and acheives what ET's.
Any pro drag car won't be using a regular setup for changing gear anyhow, so it matters not how you calssify them.
For road and track (as in for fun use not high level top fuel dragsters) it is a personal choice.