I've done some 3-D animation before. The main problems that would be caused in post-production due to having two images would be the effects shots. Aside from the fact that they would have to be rendered twice, when they interact with live-action, they have to be perfectly aligned or else the 3-D won't work.
I've also looked at some 3-D TVs and the cheaper, passive ones worked so much better than the very expensive shutter ones. The shutter glasses caused eyestrain and made everything but the TV flicker. And the picture looked rather flat as well.