The first actual Pokémon game for the Nintendo 3DS has been officially confirmed by the Japanese Pokémon website. Its name will be Super Pokémon Scramble and it’s a sequel to the WiiWare game Pokémon Rumble (known as Pokémon Scramble in Japan). The game is due for release on July 28th in Japan and it will be priced at ¥4,800, meaning it is a full-price game, unlike Pokémon Rumble. As of now, we know it will feature single player and local multiplayer modes, no mention about Wi-Fi support.
Here are some prerelease screenshots posted on the Japanese site: