Although the glasses were a factor, I don't think 3D cinema would have been significantly more successful if it didn't require them. There are other aspects of it that lead to visual fatigue that are not directly related to the glasses.
There isn't the same visual fatigue from the 3D nature of VR, because it matches your natural perspective. When I'm using VR, I am not constantly thinking "this is 3D", because it just looks like my natural vision, but not as sharp. The main area of possible fatigue would be from the vergence/accommodation conflict, but that shouldn't be much of an issue if you are displaying mostly 2D windows at the distance that Apple showed.
I'm not sure what a movie formatted for VR actually means, unless it's realtime CG. Two camera stereo breaks down as it covers more of your FOV. It doesn't respond to lateral head movement. What would set it apart from traditional 3D cinema?