http://www.officialnintendomagazine.co.uk/article.php?id=23407
Nintendo President Satoru Iwata believes that Pokémon fans will look forward to viewing their Pokémon in 3D when the new Pokémon game is released for the new handheld console.
Iwata revealed that a new Pokémon game is coming to 3DS last week and while he hasn't given much away about the new game, he did say that there will be features that work well in 3D and others that will be fine in 2D.
"Naturally, we expect 3D viewing to become one of the attractions when the new Pokémon title is released on Nintendo 3DS, but a number of other attractions, which do not depend upon the 3D aspect, shall also be realised. I have no hesitation about the prospect that a Pokémon-franchise title will be released for Nintendo 3DS."