I think a lot of our defensive struggles right now have to do with our inclination to double/trap as often as possible. I remember D'Antoni practicing that during training camp. Obviously the goal is to force turnovers and get out on the break, but more often than not, all the doubling we do is leading to broken defensive rotations where teams end up either finding the open man, or our defenders are scrambling to keep up with the ball movement.
Moreover, it seems D'Antoni wants our perimeter defenders to play up close and harass the ballhandler...and if they get beat off the dribble, Chandler/Amare/Turiaf have to be ready with the help defense (which they've done a good job of this year). But a lot of times, this strategy backfires cause once our perimeter D breaks down and Chandler/Amare/Turiaf have to step out to help protect the paint, their man becomes open for the easy dish/cut.
Honestly, don't know why we don't clog the paint more often, especially in the 4th. Dare teams to beat us with jumpers, like they do to us.