Yep, when I stop moving at all and find the sweetspot the 3D looks great. Then when I start moving and actually play the game, all I get are double images. It's pretty much unplayable to me. Conversely I have no such problems with a game like SML3D. It seems to be less of an issue on the smaller 3DS than the XL, but there's no way I'm giving up the big screens. I'll be fine playing the game in 2D.
Τry lowering the 3D intensity, it might be more forgiving when moving. I think this is one of the games worth playing with 3D turned on...(Imagine a Metroid game with so good 3D and graphics...)