There's actually two different 3DS versions. The physical boxed copy, which has full 3D graphics (models instead of sprites). And then there's the e-shop version, which is basically regular cave story.
I have the boxed copy, mainly because I got it when it first came out. Some hardcore fans don't like it though, since the camera angle is a bit off and it's kind of difficult to tell where all the edges and hitboxes are.