They would have to reprogram all games to not use that hideous red and black color scheme. It strains the eyes and just plain hurts to look at.
I don't think they'd have to do that--they haven't colorized Game Boy games, for example. They went with red because it stood out more against the black background and created sharper imagery. I actually don't mind the colors as much as the horrible position I have to put my body in to play the Virtual Boy. I showed it to my son recently and we sat and played Virtual Boy games for an hour.
Ha, maybe they're waiting until Oculus Rift is out or the New 3DS to do it. It's all a crazy scheme by Nintendo--make sure the 3D works before putting Virtual Boy games on the thing, and then capitalize on the Oculus hype by showing "we totally did this back in the 90's--look how ahead of the curve we were!"