4. Kirk's Demotion
One of the biggest problems with the ending of the 2009 movie, was the fast rise from suspended cadet to Captain for Kirk. Given the events that occurred it would have been more appropriate to give the Captain's chair to Spock, in fact. Here we backtracking appropriately to see that Starfleet command even thinks that he rose too quickly. Limiting his ship and crew to survey missions, they are seemingly testing the brash Captain and he failed one big test. So he was given the keys to flagship with provisions it seems, it's just good to see that superior officers would have misgivings about the young untested Captain. By this film's end Kirk is literally and figuratively re-born a better leader and Ship Captain, showing intelligence and wit under duress but above all understanding the humility that comes with command.
3. Special Effects
CGI use is so rampant these days that it is rare to hand out praise for work so well done and rendered. So give the Special Effects team by ILM credit for crafting some great technology and places in this movie. Both San Francisco and London look like sprawling future Urban metropolises. The revamped TOS Enterprise never looked better flying and fighting its way through space. Finally, the USS Vengeance is the most intimidating Federation vessel this side of the Defiant. if you ever wanted to know what Enterprise-D would look like in a highly militarized parallel dimension, now we have some idea.