It would probably be compatable with the DS versions, just like Colosseum, XD, & Pokemon Ranch were, although it may contain two save files, each with varied Pokemon;
Although, they may have said they weren't done with Gen V, but still done with Unova, meaning another new region may make its way on two versions of the game in Gen V, or the 3DS will have enhanced versions of Black & White, instead of an enhanced version of the game.
I hope they make Ruby/Saphire remakes with Emerald elements, and I calculated that they could do it with version exclusive areas, such as Magma/Aqua hideout, Seafloor Cavern/Undersea Volcano, the third version would be a 3D Electric Pikachu version