really bad double image and flickering on new 3DS

There's a calibration section. Personally didn't have to use it, but perhaps it can be useful. Also, the double image is a stereoscopic enigma referred to as "cross talk", if it is what I think you are seeing. That is more game specific. Both 3D Zeldas have it--it helps turning the 3D down a bit.

As Heirren said, play with your calibrations and level of 3D to see if that helps. If not I can only think of a few other possibilities.

1. Faulty system. It sometimes happens. When I got my launch Wii U it couldn't read discs so I had to send it back to the shop I bought it from and get a new one.
2. It could be your eyes. I'm short sighted in my left eye (not bad enough to need glasses but it's there) and 3D just doesn't work at all for me as a result and instead I always see a double image.

yea that ghosting is still there...even if you are in the sweet spot....

seems that is still one of the issues with the 3D.

luckily it only happens off and on but yea its there. usually in dark areas only.

you shouldnt have flickering though.... try playing you 3ds while sitting this is how the 3D works best.