One of the issues people have with 3D displays, or more precisely, rather one of the issues people’s brains have with 3D displays, is that your eyes remain focused on the same plane (the screen) while the actual visual cues change and make you think you should be refocusing. It’s such a fundamental response that it can’t really be avoided, only accommodated. One project attempting to do this is detailed in this slide from Microsoft Research’s TechFest going on right now.
The idea is that instead of having the eyes looking at the screen and attempting to focus nearer or further from it, a microlens array is interposed, which refracts the light in such a way that the eye would be able to focus on where the displayed object would actually be.