Each of the films have their good points and their less than stellar ones.
ST09 was fun to watch. My two main gripes with it are Kirk's fast track to the captain's chair (they could have missed at least 8 years rather than 4) and Nero who was so one-dimensional that he makes even Shinzon look like a fleshed-out character. Those two aside, it was, as I said, a fun movie.
STID was, for me, a far more enjoyable movie the second time around, when I knew what to expect. The Augment storyline was fine, but having Khan there seemed pointless. His only reason for existence was to have the TWOK reversal make sense at the end and to force nuSpock to contact Prime Spock. But I did like the way Khan and Kirk had to team up to beat Admiral Marcus. The Carol Marcus stripping scene was stupid. Cumberbatch is a fine actor, and I think he did a great job as Harrison. But having him become Khan wasn't necessary. I thought it was a shame Bones was reduced to the sidelines in this one.
I've only seen STB once, but I remember feeling like they were finally on their 5-year mission and that the crew had more or less settled into their characters and jobs.
When I saw the movies in theater, I was most disappointed with STID and happiest with STB, but we'll see which one of them I enjoy most in future rewatches.