McDaniels isn't inherently bad or anything so extreme...
I've just always hated how he so often calls for Shotgun-Empty formations against Rex Ryan's Defenses. He did it way, way, way too often today. Even before the fumble. You've got two Tight ends that you can use to chip before their routes. Why spread them out and take away their blocking potential? The empty sets were why Brady had so much trouble getting the play off before the clock. It why there were so many ugly passes under duress. The sack-fumble was just waiting to happen.
Really, McD got away with it in the 1st half because Rex was hesitant to overload and blitz.