The body is a very complex structure that CAN and DOES adapt to anything you put it through. IMHO it doesnt matter which diet you are doing you have to change it to keep making changes to your body.
I dont completely disagree with the atkins diet. It just doesn't fit in with a bodybuilders diet. If you are a complete fat bastard (as I WAS) it can be a great stepping stone to get you away from eating take away food for starters.