I'm not only a TG Daily contributor, but a reader as well. Trying to stay on top of whatever Star Trek news is going down, I checked out CB Droege's update where JJ Abrams talked to MTV, and gave another little tease of information to eager fans.
In the story, Droege wrote, "No word yet on the relative number of lens flares, but at this point, I hope they keep the lens flares coming in the next film."
The 2009 Trek was indeed lens flare happy, and for those who aren't cinematography inclined, lens flare basically occurs when light bounces off the lens and causes a reflection. Apparently the Trek lens flare has been a running joke for a while now, to the point where they even did Lens Flare the Movie, facetiously directed by JJ Abrams, on Funny or Die.
As Abrams told IO9, "I wanted a visual system that felt unique... I know there are certain shots where even I watch and think, 'Oh that's ridiculous, that was too many.' But I love the idea that the future was so bright it couldn't be contained in the frame... I want [to create] the sense that, just off camera, something spectacular is happening."
Back in the late '60s and '70s, the cool thing to bring to a movie was a documentary feel, so camera imperfections like lens flare would be kept in the film to make a story feel more like you were watching real life.
As pointed out in the '70s cinema chronicle, Easy Riders, Raging Bulls, the New Hollywood experimented a lot of cinematography, and where things like lens flare would be cut out of films, movies like Easy Rider kept it, creating a new style of cinema vocabulary in the process.
This was also the time The Godfather broke new ground by shooting very dark with low light levels, which wasn't done before because you wouldn't be able to see it in the drive-ins.
With the Godfather, studios then had to make two sets of prints, a lighter one for drive-ins, a darker one for theaters, though this isn't a problem anymore with the drive-ins gone. (The new digital Red cameras can also shoot at very low light levels, something David Fincher obviously loves with his movies).
Since Star Trek has made it such a part of the franchise vocabulary, there will definitely be some geeks who are going to go crazy if the lens flares aren't there. You also know there will probably be fans laughing in the theaters once they start showing up again, a joke you won't have to be a regular subscriber to American Cinematographer to understand.