Changing the angle of sprites is difficult. And that's the main reason the 3D effect would be kind of useless. 2D-based graphics CAN pop out at you, but here it would just be used for a greater sense of depth.
HOWEVER, it would indeed be great to have a decent port of the game with all the content intact on 3DS. Regardless of the 3D. I'm not THAT interested in the 3D effect at all. If games look considerably better in 2D mode (anti aliasing and added special effects), i might just play in 2D mode usually. I'm interested in the games, not the 3D as much.