Even though you can communicate with other Nintendo 3DS systems throughout the world via Street Pass you’re unable to wirelessly share game data with a system from a different region. One of the guys over at Siliconeria tried to set up a wireless battle in Star Fox 64 3D between his American 3DS and his Japanese 3DS and the two units just would not connect with each other.
Will there be a patch that fixes this problem? Time will tell.