The only issues I've run into are:
Game requires more movement / it's harder to hold still so the image will split.
2D dead spots on edges, I doubt this could be avoided, and it's not usually noticeable.
3D is a bit overwhelming, which makes me turn it down or off (I've noticed this more in games with a shifting camera.
The best 3D game is probably 3D Land, it never overwhelms but frequently amazes.
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