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Old January 11th, 2013, 05:48 PM
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Arlo
 
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I've never bothered with it myself - the only things I've done like that are transferring the best pokemon from one gen into one game (Emerald in gen III, Platinum in gen IV and I haven't done it yet in gen V) so that I can restart the other games. I always catch and use new pokemon in new games, so there's never any reason to transfer between gens.

That said, I would presume that transfer will be possible between the DS games and the 3DS games. Really, the only thing that would make it impossible would be if they make some fundamental changes to the pokemon themselves - like the special stat split between gens I and II or the addition of natures and abilities between gens II and III.