The first lens flare meme in filmed entertainment that I recall was in Babylon 5's CGI scenes, and we mocked that even though we loved the show and we weren't film students.
Whether this was intentional or not, lens flare served a rather useful function in early Babylon 5 episodes -- it subtley said "you are not here". Which is fair enough, because you're never going to be floating in space watching shuttles approaching a space station with your naked eye. Early Bablyon 5 was based on the station, and shots outside were establishing shots, or "meanwhile" shots of an incoming spacecraft presaging the latest crisis, or someone leaving, marking resolution. But the viewer, as an observer of the action, was rooted firmly on the space station. In Babylon 5, the action came to you (or at least in the first series or two... the series did lose something as it got older, was it a concidence that it lost momentum when the main characters started flying around in spaceships regularly?
So in a sense, JJ Abrams is being slightly daft and missing the point. By trying to create "immediacy" and "authenticity" by mimicking the look of fly-on-the-wall documentaries, he may in fact be losing it by removing the audience's illusion of being an actual fly on the wall.