Really, there will be sufficient storage for 3D or semi-3D if they want it *and* for all the previous regions, plus new areas.
The screen resolution isn't dramatically different on the DS vs the GBA, but the colour resoltion is another magnitude better. I'd expect prettier, animated 2D sprites in the battles and pokédex, with 3D effects for the walkaround, because I reckon that will work best on the platform. However, a 3D pokémon is a lot simpler than characters in other games; many are spheres with limbs (or not, as in the case of Voltorb).
Perhaps an option to flip between traditional top-down 2D and a panoramic 3D view of the terrain (with the double screen, you could have both at once). Scenery is a lot cheaper to do in storage terms than characters, especially if they go for a cartoon look.