additional information:
the UPCs are the same, but the flaps inside the box at the top are different. The variant is identified as NES-XR USA-1 while the normal box is NES-XR USA. Additionally, the right side of the variant box says "For sale and use in the USA, Canada, and Mexico only" underneath MEGAMAN 2 in white letters; this is not present on the original box. The REV-A identifier on the variant box is in white, while printed in black on the original.
Also, on the right tab on the inside is a number printed in gold. My original box has the number 91109, and the variant has 20311. @matt, what is the number on your variant?
They also seem to be different colors. The original is more of a purple dominant color, while the variant is more of a blue dominant color.