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The official Japanese site has detailed that pre-orders for the upcoming game, Pokémon Super Mystery Dungeon, are set to open on July 4th. With this, they have announced three different pre-order bonuses which will be available if you pre-order the game.
First, if you purchase the physical or the download copy, you will get a Nintendo 3DS theme featuring the package illustration drawn by Ken Sugimori
Second, if you purchase the physical version, you'll get a set of 3D stickers using illustrations from the box art, also drawn by Ken Sugimori
Finally, if you purchase the download version, you'll get a second Nintendo 3DS theme for your home screen