I liked both equally, but I reckon Into Darkness was better.
Honestly, 2009 had a better pacing to it and it felt fresher but was weighted down by some poor character judgement (by which I mean the villain was weak as all mighty hell).
Into Darkness had a better villain -Cumberbatch nailed it. I reckon he had far more depth than both of his predecessor although I don't think he nailed the revenge aspect I also don't really think that was the point of this literation of the character- this time it was more about family.
Family being said, the crew worked brilliantly as well and the Spock and Kirk scenes, especially when Kirk saves everyone was brilliantly acted.
I also really liked how they didn't kill Harrison at the end. That's a nice change from the standard blockbuster (Only other two I can think of like that was The Dark Knight and the Avengers).
Also, I love that Carol Marcus is part of the crew now. Really love that. The core crew needs at least another women and I'm so happy that's happening. I look forward to seeing her back.
I reckon the script in Into Darkness was a slightly a bit worse but that's mostly because they really upped the fanservice and I'd be lying if I said I didn't like it.
I'm a fan of good script work which is probably why I enjoyed both equally. Overall though I reckon Into Darkness was better simply for the acting and the character work.
Also, loved the empty getting blown to pieces at war, that was some beautiful work.
The Klingon looked awesome as well. Actually alien, well more alien. And it was nice to see that they're still suffering the Worf Effect. Getting their arse handed to them to prove just how badass the villain is. It wouldn't be Star Trek without it.