I have only watched Into Darkness once compared to the multitude of times I have watched Star Trek so I can't make a fair assessment until the Blu-ray/DVD is out.
However, I will say I strongly suspect Into Darkness to come out on top. It had stronger characterization and a more profound, deeper story. 2009, ultimately, was a Spock movie, but STiD gave a lot of depth to Kirk as well, which I felt was sorely needed.