Thought i'd jump in with my two cents. Wrath of Kahn is my favorite of the feature films, and i can tell you it's not due to nostalgia. I only first watched the film about 7 years ago, when i was 19, i think.
For all the aspects of the film that now show their age, i find it still far more exciting than even the latest films. Kirk versus Kahn feels like a true battle of the wits. Kahn feels truly ruthless, cold and determined in a way that greatly trumps John Harrison in the latest film, no matter how much Cumberbatch elevates the character. Plot points are picked from the originals, because they're cool and don't feel earned and the level of fan service gets ridiculous.
I especially much prefer the final act of WoK, which feels truly tense and as people have already described it, like a submarine or chess battle. Into Darkness succumbs more to the dumb action ending, which the RLM guys talk about every film needing to end with these days.
For the record. I've actually very much enjoyed both of the Abrams films. 09, more than STID. Abrams obviously has his heart in the right place. I think like most people concur around here, he's obviously being held back in the writing department. Which is why i'm excited to see what he does with Star Wars Episode 7, paired with Michael Arndt.