I think the debate about whether 3-D works or not will never die.
Any article (like Mr. Murch's) that attempts to use scientific means to prove the point as a matter of factual statements is going to be controversial, because, I think, it's really an opinion question. Some people really love the 3-D experience. Others don't. Probably most people are more in the middle, or not so firmly entrenched in one position that they're not willing to give a movie a try if it seems important enough or popular enough to give it a chance. I think a more apt comparison, rather than comparing 3-D to the advent of color in film, might be the creation of surround sound. (Obviously surround sound won't cause eyestrain, but as far as a personal enjoyment thing goes, give my comparison a chance.) Some people love surround sound to the point of having the best quality setups in their homes; other people are perfectly content with their TV's stereo speakers. To some people, it's the kind of enhancement that they can't live without; to others, it's something they barely notice or care about. Few people would argue that a movie originally recorded in surround sound couldn't be enjoyed in regular stereo; I think it's more or less the same with 3-D. The content is still the same, it's just how it's presented. I like surround sound a lot, but at the same time, I have absolutely no problem watching a movie downmixed to stereo.
(I'm sure my dad and my brother would be very happy never to see a 3-D movie again, and yet, when Avatar came out, they decided to see it in 3-D because it was a big enough event that curiosity and (mostly) rave reviews got the better of them. And basically they walked out saying, ehh, liked the movie a lot, the 3-D didn't really make a difference to my enjoyment, which is probably the most I could have hoped for in terms of response.)
For the record, I love 3-D. It doesn't strike me, usually, as making something seem more realistic - it just engages me in a different way. I was fortunate enough last summer to see a bunch of 3-D films from the 50s being projected in dual 35mm at the Film Forum at NYC, and I have to say, "House of Wax" was just incredible. (Also, much credit to the Forum for not charging a single penny extra for those films being shown in 3-D. Even though the projectionist had to work a lot harder than a normal day to keep those 35mm reels in sync, a situation that would actually justify charging more, they didn't. Because a movie ticket is a movie ticket, and price shouldn't be determined by content. Can you imagine if someone said, "all 90 minute movies cost one price, but if you want to see a two and a half hour movie, that costs extra"?) By no means the best movie ever, but I was sucked in from start to finish. I enjoy the process enough that at times it will make me interested in seeing something that doesn't normally appeal to me. I can also understand why people don't like it, because it generally is a very stylized way of looking at something. I've never had complaints about wearing the glasses. (I always think in response to people who complain about the glasses, well, how would you propose to make each eye see a different image simultaneously?) But, I'm someone who wears glasses normally so I'm used to having them on my face. It's maybe a minor distinction, but if you're someone who normally doesn't wear glasses, just the sensation of having that foreign object on your head in a situation where you're not used to it probably is weird.
There are a couple little things I found ironic about Murch's piece and Ebert's posting of it. The first is that Murch seems so opposed to the medium of 3-D as being unnatural, etc., and yet, he was one of the pioneers in multi-track sound. Interesting to have someone who's so forward thinking in one aspect of the medium and so dismissive of another aspect. And with Ebert, often in reviews of 3-D films he complains about them being too dim, or says that sometimes he takes his glasses off and marvels at how much brighter the image is. To that, I have two comments, the first being that as Ebert is well aware, a lot of theaters have their bulbs turned too low in a mistaken belief that it will give the bulb a longer life. Surely that must be the case in some theaters screening 3-D; sometimes the filmmaking process isn't the problem, it's the exhibition that is. The other thought is that 3-D movies are color corrected in a way to compensate for wearing the glasses (so that 3-D prints of the same film will be timed differently than the 2-D prints, with the idea being that each viewed in its proper projection will both be about the same), and that 3-D projectors are generally turned up to make up for light loss - in other words, of course it's brighter when you take the glasses off, but it's also far brighter than what the filmmakers would have you watch in a 2-D presentation.
But again, and I have great respect for Mr. Murch, Mr. Ebert, and all of the posters here, I think this is something that cannot be settled based on factual observations alone. Factual observations can explain why some people react badly to 3-D, as well as why it's not truly "natural", but those observations cannot take away from the fact that some people just like 3-D movies. Trying to tell someone who likes something that they are, in fact, wrong in their opinion is never a conversation that goes well. It's actually a little bit rude: say you disagree with my opinion, say you don't like the process, but in any other context other than a 3-D discussion, would it be polite to tell someone that they're wrong just because you don't enjoy the same thing?
I don't want every movie to be in 3-D. Nor do I want every movie to be in color or in widescreen. I want each film to choose the process it uses based on what is best for the material. The more studios try to attach 3-D to things where it's not really appropriate to the content, the more people will discredit the process as a whole. And the 3-D conversions really need to stop. It's like watching a colorized film; at best, it almost kinda maybe looks right, but it's never as good as it could be if it was shot natively in 3-D. The filmmakers behind "Pirahna" said they opted for conversion because the 3-D cameras were difficult to use and hard to fit into the spaces they were filming in; to that, I say, learn how to better use the 3-D cameras, experiment, champion new innovation in shooting, convert a couple shots that were impossible to get otherwise, but don't plan to make a 3-D movie by starting shooting in 2-D.
Final note: someone here mentioned that how one cuts from shot to shot in 3-D is really important, and an art that's still being refined. I think the concert film "U2 3D" did an amazing job at making the 3-D experience seem accessible rather than jarring by being edited differently from most films; long dissolves instead of quick cuts, shots being held longer than the standard concert film. The filmmakers there knew they were working in a different language and adjusted accordingly. Non-documentary filmmakers working in 3-D should be more adventurous in their editing choices, and should feel free to avoid frequent quick cuts.
Ultimately, we all have to be respectful of other people's preferences and what they find their enjoyment in; people who love 3-D shouldn't call 2-D-only people idiots, and 2-D-only people shouldn't try to convince 3-D lovers that they shouldn't love it. As for the rest of the public, they deserve the opportunity to see a film shown with the best technical standards (something sorely lacking in many, many theaters) before being asked to decide their preference.