I thoroughly enjoyed both movies, and maybe it's a little too new in my head for me to give a completely objective opinion, but I have to say I enjoyed Star Trek Into Darkness more than Star Trek (2009), and since I loved the first movie, that's saying a lot.
For me, this movie has a bit better pacing, the characters are more well rounded, the further exploration of new world elements into the movie (we get to see a modern 23rd century city!) is refreshing, it has a fantastic villain who is multi-faceted and has a strong on screen presence, and some wonderfully funny moments along with a few very poignant scenes that just puts this movie over the top.