A large part of the story in Interstellar takes place in space and hence there are many occasions when it feels like "wouldn't it have been better to watch this scene in 3D?". Especially after Gravity, the expectation has risen for the space scenes? Although, I would agree that Interstellar and Gravity are very different movies. There is a lot more to Interstellar than the space scenes, it primarily being a story about humans, but still this question comes to mind "Why didn't Chris Nolan shoot it in 3D?"
Christopher Nolan is, quite famously, aghast with 3D; which he perceives to be an industry forced as opposed to audience led technology... basically, its only around as a way for the film industry to make more money. Nolan is a great advocate of Film, and a great critic of the machinations of the film industry that are pushing for 3-D:
"The question of 3-D is a very straightforward one," said Nolan. "I never meet anybody who actually likes the format, and it’s always a source of great concern to me when you’re charging a higher price for something that nobody seems to really say they have any great love for."
He has also been quite outspoken on how 3D visually diminishes the final content, as opposed to contributing anything aesthetic to it...
"I find stereoscopic imaging too small scale and intimate in its effect. 3-D is a misnomer. Films are 3-D. The whole point of photography is that it’s three-dimensional. The thing with stereoscopic imaging is it gives each audience member an individual perspective. It’s well suited to video games and other immersive technologies, but if you’re looking for an audience experience, stereoscopic is hard to embrace. I prefer the big canvas, looking up at an enormous screen and at an image that feels larger than life. When you treat that stereoscopically, and we’ve tried a lot of tests, you shrink the size so the image becomes a much smaller window in front of you. So the effect of it, and the relationship of the image to the audience, has to be very carefully considered. And I feel that in the initial wave to embrace it, that wasn’t considered in the slightest.”
Christopher Nolan has repeatedly expressed his dislike for 3D based on various reasons:
For example in an interview about Inception he expressed that while interesting, 3D isn't too relevant for a movie's effect:
DEADLINE: Why didn’t you shoot in 3D which studios like Warner Bros have made a priority?
NOLAN: We looked at shooting Inception in 3D and decided we’d be too restricted by the technology. We wouldn’t have been able to shoot on film the way we’d like to. We looked at post-converting it, actually did some tests, and they were very good. But we didn’t have time to do the conversion that we would have been satisfied with. Inception deals with subjectivity, quite intimate associations between the audience and the perceived state of reality of the characters. In the case of Batman, I view those as iconic, operatic movies, dealing with larger-than-life characters. The intimacy that the 3D parallax illusion imposes isn’t really compatible with that. We are finishing our story on the next Batman, and we want to be consistent to the look of the previous films. There was more of an argument for a film like Inception. I’ve seen work in 3D like Avatar that’s exciting. But, for me, what was most exciting about Avatar was the creation of a world, the use of visual effects, motion capture, performance capture, these kinds of things. I don’t think Avatar can be reduced to its 3D component, it had so much more innovation going on that’s extremely exciting. 3D has always been an interesting technical format, a way of showing something to the audience. But you have to look at the story you’re telling: is it right?
In an interview with The Telegraph he said that he is still sceptical about the whole technology, that he doesn't enjoy it as a viewer himself and that he thinks many viewers agree with him:
When we talked about his movie Inception and why he decided not to convert it to 3D, he told me: “3D has come and gone many times over the years. I don’t particularly enjoy watching films in 3D because I think that a well-shot and well projected film has a very three dimensional quality to it so I’m somewhat sceptical of the technology.
“Until we get rid of the glasses or until we really massively improve the process, I’m a little weary of it.”
He also is of the opinion, that it is mainly a way for studios to charge higher ticket prices, something that he, out of respect for his audience, just doesn't want for his own movies:
“The question of 3-D is a very straightforward one,” Nolan said in a recent interview. “I never meet anybody who actually likes the format, and it’s always a source of great concern to me when you’re charging a higher price for something that nobody seems to really say they have any great love for.
“It’s up to the audience to tell us how they want to watch the movies. More people go see these films in 2-D, and so it’s difficult data to interpret. And I certainly don’t want to shoot in a format just to charge people a higher ticket price.”
And in an article about Interstellar in particular, he explains that while he still likes to embrace new technologies (for example he's quite an IMAX fan), he feels that digital and 3D is not the best way to capture images for him:
The “Interstellar” filmmaker confessed that he is not a fan of 3D and prefers to shoot on film, not digital. “I'm committed to film not out of a sense of nostalgia,” Nolan said. “Film is the best way to capture an image.” He's not a luddite, he claimed. It's just that images aren't as sharp and can appear pixilated when projected or shot digitally. “I'm in favor of any kind of technical innovation…for me it always has to exceed the technology that came before it,” Nolan explained.
Nolan argued that studios are more interested in bottom lines than beauty. Digital copies of films are less expensive to produce and ship to theaters than 35 millimeter copies of films. He suggested that studios are willing to accept technical imperfections “in the drive to make things cheaper.”
Not all 3D is bad, Nolan argued. He praised Baz Luhrmann‘s “The Great Gatsby” as a film that used the extra dimensionality to great effect and created an atmosphere that washed over viewers. Yet, it can also have an isolating impact, Nolan suggested, one that removes viewers from a communal experience of moviegoing. “My resistance to 3D is purely based on what I feel is right for the films I want to make,” Nolan said.
As a little addendum, I just watched Wolfgang Schmitt's interesting analysis of the movie and he also makes some remarks about the movie's and Nolan's sticking to analog 2D, setting it in relation to the minding of at least some traditions while still venturing into new territories present in the movie's story, as well as the pragmatism and anglo-saxon philosophy supposedly inherent in the rest of the movie (translated into English by me):
Nolan is an advocate of the analog cinema and this materiality of the film is also reflected aesthetically. It's the little impurities, the rouhgness of the images from cinematographer Van Hoytema, which makes the screen actually look like a screen. There doesn't reign a photoshop-highgloss aesthetic here, the screen doesn't become a slick user interface. There is really still sweat on Cooper's face, the space shuttle doesn't look like being cleaned daily by a cleaning sqaud...
...But it's also about tradition and origin. In the movie there's a careful evaluation of what has to be kept and what can be removed for standing in the way of progress. [...] Books still play a large role, and not everything that's new is good, for they shy away from the act of just reproducing the humans artificially. The human as he is is alright, the movie wants to say, enough potential is in him and he too can reach new dimensions without sacrificing his being human. What holds for the humans also holds for cinema. Christopher Nolan, the upright fighter for the alalog cinema shows us what is possible with the classic film stock. Like the good old book shelf can be a key to new galaxies in the movie - one of the most beautiful homages to the printed book one has to say - in the same way in the good old cinema there's still new things to experience. But the real new things are only possible when there's also something kept. Of course Christopher Nolan doesn't need 3D glasses to show this, as he's long reached the 5th dimension anyway.
One thing that hasn't been mentioned here yet is that Nolan is also unhappy with the technical limitations of existing technology, namely that 3D movies are significantly darker:
“On a technical level, it’s fascinating,”, “but on an experiential level, I find the dimness of the image extremely alienating.”
The 3D process, Nolan said,
makes “a massive difference” in the brightness of the image. “You’re not aware of it because once you’re in that world, your eye compensates – but having struggled for years to get theaters get up to the proper brightness, we're not sticking polarized filters in everything."
(shamelessly borrowed from this answer)