There is a kind of ghosting, that is 100% the hardwares fault/flaw, and can not be solved by the consumer. (Other then turning to 2D)
It's when bright objects are close to drak objects.
From the picture on the back layer, the bright parts will shine through the front layer.
This cant be fixed by turning down the screen brightness, and can only get reduced by sliding down to less 3D.
Like bright Sunlight can make you see both layers with both eyes at the same time, the light of the layers itself can also do this for parts of the image, where you can see bright objects next to dark.
Like standing with Link in front of a big black door(in Zelda : OoT3D), in the lost forrest. If Link will stand in front of something big and dark, it's the easiest way to see this ghosting.
I think it's mainly right-shifted.
I also see it for ex. when looking at the death mountains halo at night, or well, a lot bright stuff is ghosting at night.
(I also notices this in Pilot wings resort, for ex. when seeing a big golden ring in front of a dark-brown mountain.)
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When I bought the 3DS, i knew, it might be a challange, to always keep focus, and hold my hands still.
But this is a design flaw of the 3DS, that for me means, that this console is not able to completely & correctly display 3D graphics under all circumstances, even if you play under the best conditions, and have no fault.
Im very pissed, because I'l bet my ass Nintendo knew about this long ago.
So I can come up with only 3 solutions:
1.I have to learn to ignore this kind of contrast-ghosting. (pretty hard, because is p. me off every time i recognize it)
2. I have to turn the 3D very low, to see less ghosting, or 2D to see no ghosting.
3. Gamedesigners have to make only very bright and colourfull games, and avoid the colour black, like the black death.
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Yes, it's often the consumers or consumer's eyes fault, why people see ghosting.
Still, there is the kind of ghosting, i and others explained here that is definitely cause by the construction of the 3DS's upper screen alone.
And this shouldn't be. It also shouldn't be publicly ignrored, by always blaming the consumer, to protect our beloved Big N.