No doubt there is a "cool" factor to 3D cameras, but they are still a tiny fraction of the camera market. Given that they are apparently only able to offer one type of camera, and want to keep the price to a minimum, and want the widest range of applicability it seems to me a basic 2D camera will be chosen.
Although the GPU can support two cameras at the same time, the Raspi board only exports one CSI interface to the connector. So 3D isn't possible as standard.
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MIPI CSI-2 has amazing bandwith, and the VideoCore IV is blisteringly fast when accelerated with appropriate drivers. Would it not be possible to run two cameras through one port?
Yes, you could.
You would need to use a CSI multiplexer chip like the FSA 642 from Fairchild.
But you would also need to tweak the drivers to have one camera running at a time which requires access to the GPU code.
The firmware doesn't properly support multiple cameras right now (or even one, on the compute module). Although changing it to be able to use both cameras at once isn't hard, doing so properly would take a while. But yeah, you should be able to use the compute module to access both cameras at the same time (eventually), but I don't know how practical it will be for 3D video.