the 3d works but its too complicated to use for a portable device. I used it a bit when I first got mine with Animal Crossing and 3D Mario Land and its neat but you have to hold it at a specific angle which is not comfortable for me and also my eyes start to hurt shortly into it and I can feel becoming crosseyed if I keep it up.
I dunno if its my copy but the new Pokemon almost has no 3D effects at all for me, only when Im in the pokedex or other certain menus.
Only the standard (1v1) battles are in 3D as far as I know.