I hope so.
At least in terms of the overworld, there's so much camera angle stuff and cutscenes going on in BW that switching to rendering everything polygonally will greatly improve the effect if they keep doing that, getting rid of the messy sprite scaling and jerky rotation of the sprites. It also opens up the possibility of even more camera trickery for angles that would down-right impractical in sprites, and makes it much easier to ditch the four-way movement in favour of a full 360 degree radius of movement, which can be achieved using the 3DS's analog stick.
As for battle sequences, well, the sprite animations themselves aren't going to get much better thanks to the immense amount of work needed for animating sprites - which coupled with the work Game Freak would need to put in anyway just to draw larger sprites to fit the 3DS's higher resolution (and much wider) screen makes 3D battle sequences a very attractive alternative to keep improving the quality of battle sequences, along with allowing for more interesting camerawork.
If both the overworld and battle sequences use 3D graphics it also helps to share 3D assets between them, rather than drawing different sprites for characters when they're on the overworld or they're in-battle.
