As of now, I have seen Star Trek Into Darkness twice. On my first viewing, I enjoyed it pretty well. On my second viewing... I liked it far less.
Into Darkness is a well-directed action film with plenty of thrills and explosions. The special effects are generally brilliant, the sound design is excellent, and the cinematography is very good. The script, however, is clichéd and pointless. It meanders about its major points without actually making them, and even basic logic seems to be less important than getting to the next scene so we can see something else blow up.
Even the character arcs don't make sense. Kirk is supposed to be learning a lesson, but most of what he does is find more and more clever ways to beat up the bad guys. At absolute most, he learns a lesson about self-sacrifice, but self-sacrifice isn't his problem; it's recklessness. He doesn't learn anything of value in this film.
Spock is no better. Apparently between the last film and this one, he's shut himself off emotionally, leading to conflicts with Jim and Uhura. He and Uhura basically spend the entire movie bickering FOR NO REASON. They end up in the exact same place they were in in the last movie. If they'd broken up, then at least it would have meant something.
Speaking of Uhura, she does basically nothing except worry about Spock and argue with him. She has no meaningful place in this movie. Granted, it's the same with Chekov and arguably Sulu, but at least they have their place and they fit in it very well. Uhura seems like she's given a ton of screen time without reason.
There's also the introduction of Carol Marcus, who seems like she's only there to give exposition and make us all squeal with fan joy because Carol Marcus from The Wrath of Khan is on-screen. Except that she's hardly anything like that Carol, and is probably more notable in the movie for being in her underwear than anything else.
As mentioned, I have several major problems with Into Darkness's plot. They get spoilery, however, so if you'd rather skip them, go ahead and scroll down to the second bolded warning.
WARNING: SPOILERS BELOW
Splitting the film's villain duties between Harrison and Admiral Marcus was a mistake. All it does is rob Harrison of the spotlight, keeping him restricted. Hell, Harrison spends a third or so of the movie in the brig doing almost nothing. He's only shown in control on-screen for a select few scenes; otherwise he's nowhere near the masterful villain that Khan was in Star Trek II.
Speaking of Star Trek II, another of the big problems with STID is that it spends so much time aping The Wrath of Khan. Heck, it's in some ways dependent upon The Wrath of Khan. Lines and scenes are directly lifted from Khan, and much of the dramatic weight in Into Darkness comes directly from the audience's supposed knowledge of Khan. It feels quite a bit like what Superman Returns did with respect to Superman: The Movie, and it's just odd. In some places, it's actually frustrating. This is supposed to be a new storyline with a new crew, but it's still incredibly reliant upon the past. There's no reason to revisit The Wrath of Khan unless you're going to build upon that story, not merely echo it.
-Harrison is Osama Bin Laden: A man who believes he's been wronged by the Federation/USA and begins terrorist attacks on a major city as retribution.
-Admiral Marcus is George W. Bush: A militant leader who uses Harrison/Osama as an excuse to start a war with a third party (Klingons/Iraq) he believes to be a major threat.
-The Enterprise crew are soldiers whose lives are willingly sacrificed by Bush/Marcus in favor of the unnecessary war.
It's not the fact that political allegory is used that's the problem; it's that it goes nowhere. The answer to the entire problem seems to be "let's just blow up all our problems, unless it's to our benefit not to."
Into Darkness is a Star Trek film that seems to be asking its audience not to think. As any Star Trek fan can tell you, that is as close to blasphemy as Trek can get. The Star Trek franchise is a shining beacon of sociopolitical commentary, philosophical discussion, and inspirational metaphor. Star Trek Into Darkness is a popcorn blockbuster with lots of explosions and nothing of true substance. While this isn't a cardinal sin, it does mean that this film falls well short of the mark. It's not nearly as bad as the worst of the Trek series (TMP, V, Generations, Nemesis), but it's nowhere near the top five either. It sits comfortably in the middle, neither gaining nor losing anything. It remains a stagnant point for Star Trek, and after waiting these four years since Star Trek's 2009 release, that is completely unacceptable.