Along with the new denomination (basically, cash instead of "points") the 3DS eShop will use new prepaid cards. The designs for the Japanese cards have been revealed, and they're so cool, featuring Kirby, Famicom, Mario, and Zelda designs.
Only time will tell if the American cards will be available in awesome, Nintendo-themed variants. Actually, we can tell too. They won't. Just a guess. These are available now in Japan, and can be used for Wii or DSi Points, or 3DS eShop currency when that service launches.