According to Sony's Simon Benson, it's all about the framerate.
Movie lovers and game lovers have different needs. If you're a film buff, you seek out a television and Blu-ray player capable of giving you 24 frames per second so that you can enjoy your movie as it was intended to be seen. If you're a gamer, you'll be more inclined towards higher framerates for the smooth look.
According to Sony, that's the reason that their 3D games and 3D Blu-rays will be playing back at different resolutions. If you're playing a game, even one made for 1080p, you'll get it in 720p when you go 3D, but you'll still be getting that 60fps performance you've come to expect.
When it comes to movies, 24fps is preferred. Since the system has fewer frames to generate, it can handle the full 1080p resolution.
Two questions immediately leap to mind. First, does this mean that movies and television shows shot at more than 24fps will only be 720p when they go 3D? The other, of course, is whether anyone will notice the resolution difference once 3D is in effect.