Heck, there are even more issues - just ponder set design and many visual effects. You can't fake rain with a little water falling just in front of the camera anymore when you can
tell it's just some water right in front of the camera. CGI it? You need those CGI raindrops in three dimensions. Etc.
But it's not that 3D will never work, it's that we're clueless about how it will be made to work.
3D films are a distinct medium, not "films++". Right now, we're at the equivalent of the, "I know, let's point a single, unmoving camera at a stage play!" stage of early cinematography. At that point in time, you could come up with an analysis as good as Murch's for why this "filmed stage play" thing was just stupid and could never be satisfying - and it would be just as completely correct.
Just like you can't just point a camera at a stage to make a movie, you can't just throw three-dimensionality at a movie production to make a 3D movie. We need to develop a new craft. We need a good decade or more of people poking at this technology in a real, innovative way. We need lots of directors and cinematographers experimenting with this. Hell, we need a horde of film students making inane, pretentious shorts with rented or borrowed equipment - or even people who've never been near a film school. We need this sort of work just to get started in this new medium.