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It'l most likely be on the 3DS. Iwata confirmed a 3DS pokemon game is in the works. Black and White also added many more 3D effects to the series. It's a no brainer. Gray will probably be released in September 2012 in Japan, March 2013 everywhere else. By then DS will be in a big decline, and a main pokemon on 3DS will drive crazy sales in the 3DS's 2nd year, beginning of it's 3rd year.

On another note, it does seem like a lot of people want to see their pokemon in 3D (not talking about the effect there), while a good portion still wants GameFreak to strictly represent them with sprites. There should be an option in the options menu to switch between them to make everyone happy. =3