I have noticed that in the larger version of the 3DS(xl) the 3D is much much better. BUT I do also know that I can't for the life of me turn that 3D up much at all. It hurts so bad, but then again I also have a problem with HD Tv's and 3D movies sometimes. I think it may have something to do with a astigmatism that I have because one eye has to work twice a hard as the other. x.x;
I have trouble with 3D movies at the theatre as well as 3D TVs. From what little time I've spent with the 3DS (just demo units at stores), it seems to actually work better for me.