JJ Trek made it about characters still getting to know and understand each other, they are in their 20's and far from the middle aged veterans you see in TWOK.
Well, that's another problem. When they reused those lines from TWOK in Into Darkness, I'm of course going to immediately compare the performance to the original. And those young characters just couldn't come close to pulling off the level of emotion that those same lines had in TWOK. The characters in TWOK had years of history together, whereas the characters in JJ Trek were still getting to know each other as you said. Nothing wrong with that, but the reused scenes from TWOK just didn't work in Into Darkness for that reason. If you're going to re-use lines or scenes, you should make sure the new version is either way better or a parody. And for me, those lines came off as parody in Into Darkness. I understand it's subjective, but that was my experience with it. Plus, I just didn't like the concept of reusing the lines. I understand what they were trying to do, but it didn't work for me. Those scenes (and the Nimoy cameo) aside, I actually loved Into Darkness. Unfortunately, those scenes came at a critical time in the movie.