I guess it really depends on what you plan on doing with your car. I actually chose to get an auto in my '05 and I'm very happy with it. If you want to race, and if you like banging the gears, wait it out. But, like Sgt Beavis says, when you're sitting in traffic every morning on the drive to work, the auto is going to look pretty good.
The new auto is much improved over what was already a good auto in the SN95 cars. I had a '96 with an auto. This new one is better. Very smooth, very positive. And, by the way the difference in at least 0-60 times is only a couple of tenths, maybe 5.1 vs 5.3. Take a look in the latest MM&FF. They got some great times with an auto.
Ford has also kept a feature I like which is the ability to start off in 2nd gear. This is great for slippery conditions. And, you can also just tap the OD button to turn it off and get yourself a little engine braking before entering a curve.
But, it depends on what you want out of your car. Either way I'm predicting that you will have to have surgery to remove the smile from your face after you take your first drive in your own Mustang. It is going to be there permanently.