Uhura's bridge console
First pic is the 2nd Beyond Trailer, second is Into Darkness, third is ST09. It looks to have a few cosmetic differences, most notably different (and A LOT less) lighting. There's a few differences on the console, but nothing major.
Enterprise corridor
First pic is 2nd Beyond Trailer, second is Into Darkness. It looks like they redid the ceiling for sure, and it might just be me, but it also seems like the lighting is warmer compared to STiD.
Impulse engines
First pic is 2nd Beyond Trailer, second is Into Darkness. Doesn't look like any major changes. It might be a trick of the lighting, but it looks like the center part of the neck that goes down might be flattened.
Saucer underside
First pic is 2nd Beyond Trailer, second is Into Darkness, and third is Into Darkness as well. Doesn't look like all that much major, but it does look like the phaser emitters are in a different configuration/there are more of them.
Here's what I'm talking about pointed out.
EDIT: At the 0:9-0:10 part of the 2nd Beyond Trailer you get a nice flyby that indeed shows a different phaser emitter configuration.
Saucer upperside
First pic is 2nd Beyond Trailer, second pic is 1st Beyond Trailer, third pic is Into Darkness, fourth pic is Into Darkness. At first I thought the phaser emitters were also in a different place on top, but then I realized that the view in the 2nd Beyond Trailer is probably of the side of the saucer rather than the front. Still it looks like another phaser emitter might be closer by than would have been on the Into Darkness configuration. If so, it seems likely that the model used in the 1st Beyond Trailer wasn't entirely done being updated for the movie. Which given that none of the other graphics, doesn't seem like that much of a stretch. IDK, probably seeing things.
EDIT: The 1:05 mark of the 2nd Beyond Trailer shows a phaser emitter at a different spot of the upper hull saucer as well.