In my experience really good 3D takes into account the time it takes for your eyes to educate. Talking to one of the software designers for the film I know that was the intent, but it didn't work for me.
The best 3D I've seen was the IMAX "Space Station in 3D". Absolutely stunning. Probably the best cinematic experience I've ever had. Like floating in space, maybe, but with gravity.
DS