Even if there were real 3D, how would you make use of this properly? Current story telling only works because you can limit and control what people see. How will a horror movie work if half the audience can already see the guy hiding behind the rock before he leaps out? (This is just one example of a ton of problems that would arise)
I'm not sure that most people who want 3D know what they are actually asking for - personally I think 2D is perfect just leave it alone.
You can still have true 3D and mise en scene at the same time. True 3D film would still require a director's eye to progress the story, focus the attention of the audience, and deliver some degree us suspense and drama. One could have true 3D, and not at the same time have it basically be a Holodeck program where the viewer sees everything.