It seems GBA games might be coming to the eShop soon. Nintendo Australia’s website features a GBA Virtual Console logo under the list of Virtual Console platforms. The only title listed for the GBA so far is Dr. Mario. While Dr. Mario was released for the GBA, it was ported from the NES. As the 3DS has a NES Virtual Console, it could be referring to the NES game.
Even so the fact that there was a specific image made for a GBA Virtual Console gives me hope. Playing Mario and Luigi Superstar Saga as well as other great GBA games on my 3DS would be really awesome!