The whole thing is like a zoom lens -- you don't overuse it or it just looks like amateur hour. DIE HARD really pushes the limit for me in terms of lens flare use, but they trot them out at just the right times, when the vault opens, when the tank/rv shows up, a few other instances -- but Abrams to me comes off like a 7 year old with a zoom lens in his MIS-use of the flares.
Actually the way he uses flares is for me the exact equivalent to what we saw in the 70s when you were supposed to be in the realm of aliens on THE SIX MILLION DOLLAR MAN ... time to run out the diffusion filter to make things look otherworldly ... instead it just looks like you're trying to cover up the fact there isn't anything special on screen. The fact Seth Rogen loves them and jumped on the flare bandwagon disappoints me, but not nearly as much as seeing SCOTT PILGRIM, where every time they went into some kind of heightened reality, they switched to 2.35 to get lens flares ... I think Edgar Wright is way too good of a director to have to hang on that kind of trick.
I'd dislike the AbramsTreks just on the basis of the writing and other creative choices, but the flares alone would be enough to put me off it even if it wasn't TREK ... I'm just really glad I didn't see the first one in the theater, I'd've had to leave due to being driven crazy by them. It's too much like what I remember experiencing with too-dirty old 'hard' contact lenses back in the day.
Add to that the just plain crazy lighting in control rooms ... you'd have to be wearing shades on that bridge to be able to read a display, since there are light bulbs aimed right at you any time you turn to look at a screen. Clearly Abrams didn't want any connection to reality (like keeping the light low when you are in a CIC type situation.)