I can't remember how much it was used in Into Darkness (which is probably a good sign, I guess), but it was overdone in ST11. When I saw it the first time, it stuck out from the first scene, with the sweeping shot of the Kelvin, then the bridge.
It is mostly just the bridge/ship shots, and the CG space shots, but they're plagued by lens flares. It's one thing to want to exploit the look of natural flares for effect (which is not a bad idea), but JJ purposely added extraneous lights to the bridge literally just for the sake of flares. That's the definition of excessive, and even a bit lazy and uninspired.
Whether you understand lens flares, or just think they're ghost orbs, the average person notices them, and they're distracting. Other movies have managed to look visually interesting without hiding under lens flares, especially when your subject matter is spaceships! That's already a goldmine of visual interest.
Maybe they just needed to add more barcode scanners.....