I feel the same confused sentiment about the 3DS. I would have thought Nintendo would have delayed the game to make get it on to the 3DS, it just makes sense except that all the Pokemon fans who have DS Phats, Lites and DSi(XL) wouldn't really be able to upgrade to a new and, as far as we can say, more expensive system for the sake of a new Pokemon. My little cousins don't care if it's in 3D and it would crush their hearts, their parents wallets and Nintendo's PokeStock if they couldn't put out the 300 bucks for a new system.
In a way it seems like Nintendo's setting the 3DS up for a more streamlined, robust and mature experience. Maybe only in aesthetic though. Anyway, I really thought this would have been a 3DS title.