It negates the need for color tinted glasses, which allows for full color reproduction. I have a 3D copy of Coraline on BD, which includes reg/green glasses, it looks horrible.
Initially 3D BD films will run at 48 fps, and video will be at 60 or 120. With every other frame alternating between the left and right eye views. The glasses use a continuous piece of liquid crystal, that when energized turns black and blocks the eye opposite of the one for which the current image on the screen is intended. It'll be up to the display to synchronize the glasses with the screen, be it by wire or IR.
There's no reason that in the future displays may buffer the frames, and use other eye separation techniques. For instance for front projection, an over/under setup of two projector with a pre-processor to select every other frame and send it to alternating projectors. One projector would have a horizontal polarizing filter; the other a vertical. Then the glasses could be passive, with matching polarizing lenses.
I can think of two other ways to make use of the 3D data on the disk, but I'm hungry and going to eat now.