Is the Vader new tooling? Or just the head and hand?
I'm too lazy to scour through 19 pages...
I'm comparing the POTJ Emperor's Wrath Version and this new version as I type this, so no doubt someone will post a much more succinct version in the time it takes me to finish.
HEADS: Same mold on the outside, but seemingly different on the inside. Whereas 2001's skull glowed in the dark, 2006's skull is painted a silver and blue metallic color with some visible wiring around the spinal column in the front.
ARMS: The right arms seem to be exactly the same on the outside, with the 2001 version's hand coming off in the then-de-rigeur peg in socket method. The 2006's hand, however, comes off at the glove/gauntlet line, with the painted wires and socket underneath. You can also see some mechanisms under the rest of the arm (the elbow joint seems to be where the detailing ends in there) on the 2006 version, whereas the 2001 version is mechanismless.
CHEST: The 2001 version's chest and arms are molded in the same semitranslucent plastic as the arms and head, but the 2006 version seems to be solid black paint/plastic.
LIGHTNING!: Where the 2001's version's lightning bolts are painted on the head in a blue tint, the 2006 version's helmet relies on the extra purple lightning bolt accessory that fits on top of the helmet. I guess it's the difference between Vader looking like he's a biker with corny lightning painted on his helmet to show what a bad-ass he is, or Vader with a huge purple silly string wig on. Your call.
Also of note is that the outer cape's right side is more "flat" rather than the curve inward at the cape base on the 2001 version. The lightsabers are the same (as in the pre-AOTC, nonflared blade), as is the lower body.
So yeah, different skulls, a modified arm, different chest transparency levels, and a silly string hat. Does that help or make it worse, ruiner?