I liked Star Trek 2009 better. It felt fresher to me, despite the stale revenge plot. But with 2009 I was surprised by how good the casting was and how the new take on the characters got so much of the spirit of the original actors right. And the action scenes were the best executed of any Trek film up to that point.
With Into Darkness I think the action probably exceeds Trek '09 but that's about the only thing that does. Though while Into Darkness decides to just bring Khan back instead of going the Khan-like villain route (Kruge, Chang, Soran, Ru'afo, Shinzon, and Nero all fit to some degree into that category), I felt that's where the film lost me. The 2009 film told an original story, we never really had seen how the crew came together, and Into Darkness opted for a semi-remake of Wrath of Khan.
Trek '09 opened the door to tell new Trek stories while Into Darkness took a step backward. Back in the day, when I was first getting into Trek, one of the things I often wondered was what would it be like to match the spirit and characters of the original show with today's technology.
I think Abrams and crew did a good job doing that in Trek '09, but with Into Darkness instead of pushing forward, of telling new stories, they went back to rehashing what came before. Granted they tried to wrap it into current themes, but I don't think that process helped either storyline in the film. If anything, the big reveal took all of the oxygen out of the room, and that was compounded by aping Wrath of Khan. That being said, I liked Peter Weller's addition and the mention of Section 31. I also liked Alice Eve but thought she was wasted.
I do think that Cumberbatch did a better job in the acting department than Bana. But I still can't buy him as Khan. And the change from tyrant to terrorist might be more relevant for today's audiences, but it didn't feel like Khan to me. And I'm even going to go into the nationality/ethnic/racial change in actors.