Re: "Mission: Impossible" = "Technology: Ridiculous"
Great question! I'd say that, yes, cynicism can be warranted some of the time, but not always. A lot of factors are at play.
Regarding movies set in New York, yes, its population is a factor, but so are its demographics. Houston, Dallas and Atlanta are big cities too, but they historically aren't as big for films as the Bay Area, New York, or Los Angeles. A little over 6% of U.S. citizens live in the New York metropolitan area, but I'd bet well over 6% of domestic movie ticket sales come from that region. That reality gives filmmakers some incentive to tell stories that appeal to the ticket-buying population. As the international market has grown more important, we've seen evidence of this sort of thinking. Transformers 4 was likely partially set in China because the producers anticipated that it would increase demand there. Iron Man 3 was different in China than in the U.S.; in China, it includes scenes that showed off local attractions. So there's definitely a precedent for choosing a location because a certain part of the audience happens to live there. You can also see version of this kind of thinking in the way movies are filmed. Back in the 50 and 60s—lots and lots of wide shots, because movies were really trying to differentiate themselves from TV. Today, producers know if a movie is going to earn more money in theaters, or on TV, and since it's increasingly the latter, you see way more films that are largely a collection of close-ups—stuff created more for the relative intimacy of TV screens, instead of the overwhelming scope of cinema ones.
But the above observations somewhat conflate setting a movie in a country versus setting it into a city. With New York, it's not just the population-based appeal; it's also New York's status within American mythology and iconography. The "idea" of New York comes packaged with notions about "making it," immigrant stories, an architectural sense of spaces and style, and a million other factors. Likewise, Los Angeles has a distinct place in filmic mythology. Filmmakers set stories in these cities because of their thematic value to audiences in general, not just local appeal. The fact that Blade Runner is not only set in Los Angeles but also includes several distinctly real Los Angeles buildings adds a texture to the film's dystopic vision, for example. Likewise, you could have set, say, Big in Houston instead of New York—but would it have been the same movie? You could move The Big Lebowski to San Francisco or Miami—but would it have been remotely the same? Likewise, The Big Sleep, a movie to which Lebowksi unexpectedly owes a great deal, is a story that relies on Los Angeles as a symbol. You'll find that LA-based movies usually visualize sprawl, with pockets of corruption separate by distance, whereas New York movies tend to emphasize verticality, with the elite looking down on the conquered. The cities are, in short, a convention as much as a real location.
There are other reason for filmic bias toward certain cities—by virtue of having more people, more industries, and more spaces, cities naturally open themselves up to a different range of narratives than, say, a small town in Central California or West Texas. Granted, filmmakers can certainly tell great stories outside of cities (see No Country For Old Men, for instance), but the pace and activity of cities can be conducive to cinema, which is, after all, distinguished by motion among all of traits.
Commerce of course plays a role. Shooting in New York is expensive—upwards of $1 million per day just in location costs if you want to shut down a block in Manhattan. Consequently, Vancouver often stands in, with some CGI or second unit helicopter shots thrown in to smooth things over. Does this affect your identification, as a viewer, with the film's settings? I'd say yes, but I'm not sure what the average viewer might say. Whether a city offers subsidies can also play a role—Chicago, for a while, was getting a lot of movies by advertising itself as a cheaper alternative to New York. And the zeitgeist can play a role, too. San Francisco is a very expensive place to shoot. Only New York is more densely populated, so any time you shut something down, you cause a lot of problems. Nevertheless, more and more productions are setting up in SF, and I think rising popular interest in tech companies has increased interest in the city, which is going to look increasingly like Manhattan as Salesforce keeps building skyscrapers downtown. Lots of big movies that would have typically used New York have opted for SF instead—the recent Godzilla and Planet of the Apes movies, for instance. Then there's stuff like "Silicon Valley" and "Looking" on HBO.
Cities have also been used for ideological purposes in films, too—visions of both utopia and dystopia that rely on some link between a real location, and a cinematic reassembly. Sometimes, the cinematic city isn't a real-world city. You get Gotham instead of New York, for example. But these fictional cities still take on ideological weight by using real-world locations. The Dark Knight trilogy, for instance, was shot mostly in Chicago, with some stuff in New York and Pittsburgh also standing in for Gotham in the third film. This creates a different phenomenology of viewership, and a different set of themes around the cityscape, than Tim Burton's Batman films (which mostly used soundstages) did.
For anyone who finds this sort of stuff remotely interesting, I strongly recommend a documentary called Los Angeles Plays Itself. It's incredibly thoughtful, and frequently hilarious.