I enjoyed Star Trek 2009 better. JJ Abrams nailed so much of it with the characters while providing thrilling action. I hadn't thought anyone else could really inhabit the TOS characters but they put together a cast that did a pretty good job taking on those roles. Trek '09 wasn't perfect. I thought Nero was a bit drab and there were some questionable jumps in the story. But overall I left the theater pumped. Abrams made Trek cool for the general public in a way I hadn't seen it before.
TFA, on the other hand, suffered from its story. The characters were likeable, the action was good, etc. But the opposition was lackluster. The story wasn't original. I felt more of a threat from Nero than I did from the First Order ultimately. TFA was a whole different challenge for Abrams. I don't think the movie was going to tank regardless, in a way that Trek seemed to be on shakier ground. Too much of a hype machine around it, and he had the benefit of the doubt going into it due to a lot of people needing TFA to be better than the prequels. To me it feels that Abrams was intent on being true to the spirit of the OT and providing something for the fans while with Trek he was a little more open to changing things up, since he wasn't as emotionally tied to that franchise going into Trek '09. Nostalgia wasn't as much of an issue.
That being said, TFA is better than Into Darkness. Though I would say that Into Darkness's Khan is a better villain in terms of presence and exuding menace than Nero (though not as effective to be honest) or the First Order. Like TFA, Into Darkness trod some well worn ground, but Into Darkness was more egregious in taking from older material.
Pretty much my thoughts.
Now my hopes are on Rogue One.. only the basic story is known, it's not directed by JJ who i've always felt keeps too close to the source in both Trek and Star Wars and so far seems to be afraid to really break free and produce something other than high quality fan fiction.