I'm not entirely sure why you would make films based on a franchise that you never liked. I'm on record as believing that the first JJ Abrams Star Trek flick was a reasonable popcorn flick but it didn't share anything with the original product except some character names. That's not true for the second movie. Into Darkness (to use its weird, not-really-a-subtitle subtitle) isn't just bad Trek, it's loathesome filmmaking.
The low-hanging fruit is that the plot doesn't even try to make sense for more than five minutes at a time, but since the original series was hardly airtight, I have a number of other bones to pick, including:
Sure, much of this probably seems like nitpicks and nerd rage. I've watched a lot of Star Trek, probably more than most people, and so there are a lot of things that to me are instinctively not right but aren't necessarily invalid. I think it's a shame to lose those parts of the Trek canon (and I tend to think that Abrams' alterations are worse than the material he's replacing), but I'm hardly objective. Lance believes that he's just trolling us, and I'm not sure that's wrong.
I find the movie's general incoherence to be frustrating. But that's not what actually makes me angry.
At the end of Star Trek Into Grim Serious Incoherence, Khan crashes his spaceship into San Francisco. Hundreds of thousands, if not millions, of people are killed, but that's okay because they're not the protagonists and presumably their psychological issues were less attractive. This is, to put it lightly, not really what Gene Roddenberry had in mind when he pitched "wagon train in space" to some bored Desilu executives.
Speaking personally, I'm getting a little sick of the whole "it's been a decade since 9/11, so let's crash a flying vehicle into a city and call it emotional resonance" thing that every hack director with a render farm has been on lately. Abrams is doing it, apparently the new Superman movie does it, The Avengers did it. It's a cheap, transparent ploy to make otherwise airy summer entertainment seem important, so that critics can write that your otherwise incoherent summer tentpole flick has "real-world allusions" in it. Blowing up a planet in the first reboot movie wasn't enough, I guess.
Nowhere is that more true than in Star Trek No Subtitles Just Darkness. Khan doesn't really have a good reason to crash his ship into a major city. It doesn't particularly help him achieve his goals. He just does it because, as with every other reason that anyone does anything in a JJ Abrams movie, it's part of the story checklist they wrote before actually getting to outmoded concerns like "dialogue" or "motivation" or "character." City destroyed: tragedy achieved. On to the next setpiece!
Reboot or not, there are some things that a Star Trek movie shouldn't do, and mass murder is one of them. I'm under no illusions about the ideological purity of Star Trek, especially under Paramount's management, but I like to think that Roddenberry's vision should mean something regardless. As it is, there must be a little whirlwind somewhere around the ionosphere where his ashes are spinning. If JJ Abrams wants to participate in a little cinematic disaster porn, he's welcome to do so, but I wish he'd restrict it to some other, less established franchise. It's probably just as well that he's moving on to Star Wars: this kind of bankrupt cheesiness will fit right in there.