The new version has a few different cards that replace some of the old ones. If I remember correctly, they replaced almost all the ones that didn't quite fit the card format (e.g. Carnivorous Greenhouse, Absinthe Fairy, Carousel Fairy) with a totally different new card (the meaning may be similar, though?). I also remember there was a complete repainting of Shallow Grave.
The new version also has all images fill the card completely, so there are no more backgrounds added to the sides. I can't explain it very well, so maybe an example will help: The "I am Kali" card has a wide red border on each side of the actual painting in the old edition. In the new edition, the painting is as wide as the card - which means the image is cut off at about the card character's waist.
ETA: You can see the old "I am Kali" in
this image from the artist's website.
I know I found all images of both versions somewhere on the internet a while ago, but I don't have the link.