It had to do with the fact that McNamara wanted to have the USAF and USN use the same designations for their aircraft, and reset the USN designs, and any new aircraft at 1.
The USN didn't evidently want to ditch the attack-designation for one reason or another (possibly so the USAF couldn't dictate terms), so they simply added it. And on that note: The AD was the oldest, so it became the A-1.
FlyboyJ
I thought the F-117 was given its designation to simply confuse people?