I meant "not go over well" with the fan base, not their sales- I only referenced BW2's sales to point out how popular it is. There isn't any way for BW2 to make use of 3D, so the only benefit for it to be made (at the time it was developed) for the 3DS would be slightly increased graphics. I don't think that is a good enough reason for people to buy a 3DS solely to play BW2.
I honestly believe it was made for the DS/i because there wasn't much reason for it not to be. Generation 6 will probably have ways to actually abuse 3D that isn't confined to an app.
The same held true for the Generation 3 to 4 transition, I think. Emerald was released for the GBA despite the DS being out for a year. About 2 years later, Diamond and Pearl were released for the DS and brought with it actual wifi features (which was the selling point for the DS).
It seems to me that Gamefreak doesn't like jumping on the bandwagon too quickly, and likes to take time developing new features. I think it was a smart decision to start their venture into 3D/AR Pokemon with the Dream Radar app.