I think it's too early to tell how 3D will affect the movie going experience, but it certainly could in the long run. Many films shot in 3D have scenes specifically shot for the 3D movie goer. Some of these scenes are long, and pointless, often dizzying and extraneous, hurting the story and pacing of a film only to cater to the 3D audience. The Hobbit is probably the best (worst) example of this to date. And it's happening more and more. Many studio's could become fearful that their film won't do at all well if it doesn't have some degree of 3D component, pressuring directors and producers to incorporate the novelty into a film that does not serve the project. Even digital projection is a hard sell to many professionals in the film industry.
Sometimes advancements are good; "talkies", Technicolor, and surround sound systems like THX, all enhanced the genre. As long as it remains one possible option I think 3D can be a wonderful addition to the movie going experience if it's done right, for the right movie, and serves that film and even enhances it. But as we've seen with many forms of media (vinyl records, analog film, cameras, and television switching to digital exclusivity) the market can change formats to a degree beyond our control or even actual need, dictated by commercial viability. Because newer is always considered better, regardless of it's dubious enhancements, if any.
I'm enjoying the experiment thus far, but hopefully 3D isn't thrust upon us in a way that diminishes not just some enjoyment, but damn near all of it in some cases. The free market will dictate what comes next, which hasn't always bode well for true art.