Personally I don't get the complaining, as Pokemon game will most likely make it on the 3DS regardless. They most likely working on such title as we speak, but the company does need to release titles before the eventual 3DS pokemon game. However Nintendo will be very smart if they include a tease of 3DS pokemon within Pokemon B&C2 if you play it on the 3DS.
(Given I am sucker for anything that reminds me of snes/gb era style of JRPG).