Trek 2009 is a much better film. the story flowed better and the pace of the film, which includes the action scenes and character interactions did not overshadow the story unlike STiD.
Also the 2009 film manage to find the right balance between paying homages and ripping offs. Sadly STiD did not find the right balance.
One thing STiD had over Trek 09 was the villain. Khan > Nero.
However Into darkness is still a very good film. Trek 09 is an excellent film.
Ranking the best trek films , Trek 09 should be in the top 3 with STiD rounding up the top 5 or getting 6th place.
JJ has done good work with Trek and a lot of us Trek fans should be grateful.