6. Kirk's Sacrifice
This Might be considered controversial putting this in the good category, basically remaking the iconic death scene but I liked the role reversal of the it. With Wraith of Khan, Spock's tearful goodbye was significant in empirically proving the science officer's favorite saying "The needs of many outweigh the few" and for Kirk it was to show how winning the no-win senario really costs, that in his old age he still had many things to learn "I feel... young." In this younger timeline after cheating the simulated no-win Kobayashi Maru test, Spock says that Kirk must learn how to fear. What does Kirk say first with his dying breaths "Spock, I'm scared..." he knows fear now, him giving the last duty for any great Captain shows that the ship and his crew are the only family he has left. This time around Spock realizes he cannot bury and hide his humanity like he has done for some time. In his blinding rage right afterwards he seeks furious vengeance, all too human after all. As for Kirk's resurrection, well Spock also came back from his ultimate sacrifice, so the timeline was just balancing out? In cases like this, I for one don't care about the previous installment's history behind characters and certain scenes, just tell a good story with emotional weight with what you have right here and now, that's all.
5. Benedict Cumberbatch
I know I talked about his Khan previously in the bad section, but he creates quite a villainous character despite the misgivings I have stated. Indeed this Khan is best Star Trek villain in decades. He growls with that low booming voice, has the strength of superman, fights like a demon, feels anguish, and he's just a brute force of genetic science. He gets one of the very best proper introductions in the franchise as he takes down a squadron of Klingons, saving Kirk and company. Menacing, powerful and cunning, a true threat we haven't seen in quite a look time in either Star Trek or Sci-Fi.