Game Freak would have to be staffed by a group of lunatics to want to continue using sprite graphics in their next game - and I don't think that's the case at all.
Sprites are costly and time-consuming to draw. Every time you want to add more animations to a sprite-based game, you have to multiply your workload by the amount of new animations you want - and that will very quickly add up to an unmanageable task.
We have roughly 650 Pokémon. That means they already need to draw 1,300 new sprites to fit the 3DS's screen for front and back angles. If they want to improve the quality of animations, they need to draw animations for all of those Pokémon facing in both directions.
A lot of sprites in Black and White are modified or based on older sprites from Gev IV games - already Game Freak is having to make compromises just to achieve BW's simple level of animation.
No RPG game on the planet has fully-animated battle sequences, with sprites, and has the amount of unique playable characters Pokemon has.
Conversely, a 3D model graphic can be displayed from any angle, and can perform any animation without needing further work on the artists part. It makes their job hundreds of times easier and allows them to move the camera around in battles - performing zooms, sweeps and pans and changing the angle of the battle screen in a way that's impossible with 2D sprites.
Sprites are holding back the quality of the games in several ways that also effect gameplay
To top it all off, every Pokémon already has a 3D model made for the Wii games and Pokédex 3D. Most of their work has already been done for them.
When people really like a certain game, they tend to pay for things if it means they get to play their favourite game.
Making the same game for both the DS and 3DS is out of the option.
Firstly, it defeats the object of inciting people to buy the new 3DS by offering them something that makes them content to stick with their old DS.
Secondly, it means that Game Freak have two choices about making a game - either create two very different games, one that resembles how BW currently looks on the DS and one that takes full advantage of the 3DS's capabilities, or they can make both games that look and play almost identically to one another - look at Mystery Dungeon Red/Blue and (a very relevant example) Harvest Moon: The Tale of Two Towns for DS and 3DS.
If they go with the first option, suddenly they have to spend a lot more money and more staff to create two games at once that only share basic similarities. This isn't very good because they probably don't have that many people to manage to create two games at once and still remain at the standard of quality we've seen from Pokémon games in the past. If they take the second option - congratulations. You've got a DS game just like the one you bought last year, and a 3DS game that feels cheap and nowhere near the same level as games that were designed soley for the 3DS.
Do you really want them to make a handicapped game that lives up to none of the potential of the 3DS, just so you can still play it on your 7 years old DS?