Double posting...I know, bad form...but I just posted this on another forum, and felt it deserved mentioning here as well.
Defending Star Trek Into Darkness(with some minor criticisms):
I'll be looking at some of the more common complaints and/or WTF's I've seen in regards to the movie and trying to defend them, though I am making allowances in some cases. Let's get started. WARNING, SPOILERS FOR EVERYTHING!
Nibiru
First off, the biggest question is why was the Enterprise under water and why didn't they just beam Spock out from space. I would THINK that most Trekkies could easily extrapolate from Chekov's line about the planet's magnetic field that transporters were not very reliable, and in fact, I would wager that the only reason they were able to get Spock OUT of the volcano is because the Enterprise moved directly overhead and within a certain distance. This might also account for why the Enterprise wasn't in synchronous orbit OVER said volcano. It's been shown in a few instances that magnetic fields disrupt transporters. Now, as for the Enterprise being under water...while the transporter thing could account for that, they could have just used shuttles. So why was it under water? Simple. Rule of Cool. There isn't really any other explanation. And it was cool, but the whole scene COULD have used a little more dialog to explain WHY they hid the ship at the bottom of the ocean.
Kirk's demotion/re-promotion
So, Spock is saved, but Kirk blatantly violated the Prime Directive and then lied about it in his logs. While Spock was correct in stating that, had things gone according to plan, the Prime Directive wouldn't have been violated, Kirk still covered up everything in his log. This lead him to be demoted and have his command stripped from him. Makes sense. Pike realized that Kirk hadn't learned humility and sacrifice by legitimately working his way up the ranks. But he also recognized the potential and got Kirk assigned back to the Enterprise as Pike's first officer. Again, makes sense. Where people got irritated is after Khan's attack on Starfleet HQ that results in the death of Pike, Kirk asks for command of the Enterprise back to go after him. Admiral Marcus agrees, gives him his ship back as well as 72 advanced torpedoes to blow the crap out of Khan with. This also makes sense, as I'll detail next.
Admiral Marcus's Plans and Section 31
So, Kirk, Spock, and Scotty find out that Khan used Scotty's transwarp beaming to beam to Kronos, Kirk and Spock tell Marcus and request permission to go after him. At this time, Marcus tells Kirk and Spock about a top secret Starfleet division called Section 31. So top secret that Marcus pretty much tells them everything. Why do this? Simple. It's all part of the plan. See, Marcus felt that the only way to have a good Federation is to have a militarized one. So, he put highly advanced torpedoes on the Enterprise and ordered Kirk to go and fire them at the Klingon homeworld to kill Khan. A bit harsh, yes? Well, not if killing Khan isn't the point. See, a Federation starship, firing at the Klingon homeworld, would be an act of war to the Klingons. It wouldn't matter if the ship weren't in Klingon space or the torpedoes hit an uninhabited region. So. Marcus told Kirk and Spock all about a top secret Starfleet organization, gave them torpedoes, and told them to shoot at the Klingons. Then the Enterprise's warp drive breaks down. From here, it's all easy-peasy. Marcus didn't care if Khan lived or died. He sent the Enterprise and the trouble-making Kirk to be lambs for the slaughter. The only reason he told them everything? He didn't expect them to make it back. They were meant to die, which he would then use as an excuse to begin a war against the Klingons and building up Starfleet's military. So, in this context, it doesn't matter that Kirk had just been demoted. He was being sent to die anyways, so why not give him command.
Khan Stupidity?
Let's get the big elephant out of the room first. Khan is white. Not just normal white, but pasty British white. This was something that could have been solved in one scene. Kirk or Spock looks up the historical database and finds Khan, asks what the hell, Khan says, "Section 31 surgically altered my appearance so I wouldn't be recognized by anyone." This should have happened. Now that that's out of the way, the torpedoes. Khan put his people in them. People seem to forget that he did so to try and pull one over on Admiral Marcus. Marcus, probably correctly assuming Khan would do this, got hold of the torpedoes. Khan then assumed that Marcus pulled the plug, cue vengeance. This isn't hard to understand, really. But people don't quite get it, I guess. Now, when Khan beamed over the torpedoes? He had no reason to believe Spock would pull a stunt like that. Khan is, and always was, an arrogant, egotistical, manipulative bastard, and anyone who doesn't see that needs to rewatch Space Seed. He was manipulating the Enterprise crew from the moment he woke up. That's why I like this portrayal. It seemed more like Khan than the raving, maniacal, Moby Dick-quoting lunatic from Wrath of Khan. And on to the next Khan-related thing...
The "Magic" Blood
This has pissed a lot of people off. But here's my thing. Khan was engineered for perfection. Why wouldn't he have been given a genetic trait that let him heal rapidly and stuff like that? Everything that was done to Khan was never fully explored. Rapid healing and regeneration just MAKES SENSE FOR A SUPER-SOLDIER. Why make him superior in every way but one? As for why it worked on a tribble? I don't know. All I do know is that McCoy obviously just had a dead tribble lying around and wanted to test the extent of the regenerative abilities of Khan's genetic alterations.
Kirk's death/Spock's emotional breakdown
This whole scene pays homage to The Wrath of Khan. There's no getting around that. But it is a role reversal and very little of the dialog is actually taken from TWOK. Kirk learns humility and the meaning of sacrifice. He saves the ship and crew at the (temporary)cost of his own life. And Spock learns, too late, the value of friendship. Now, I haven't heard too many complaints about the death scene itself, but I am going to give my own opinion on it. Chris Pine OWNED that death scene. I could feel his heartbreak in knowing that he paid the ultimate price for victory. Definitely a much better death scene for James T. Kirk than in Star Trek Generations("Ow, I'm under...a bridge...and I can't...get up!") But where some people gripe is Spock's emotional breakdown afterwards, and I think this gripe extends back to the 2009 film. Spock has trouble with his emotions at times. But let's look at it closely. In the 2009 film, he was fine up until he watched his mother perish in front of him and then his planet imploded. I don't know about the rest of you, but I sure couldn't stay in command of my emotions after that. And Kirk deliberately poured salt in that wound. Yes, they made up afterwards and everything seemed to be hunky-dory, but the thing is...that kind of wound will not close. This Spock is never going to be as emotionally controlled as Spock Prime was at that age. And watching the man that saved his life out of friendship die trying to save Spock and everyone else on the Enterprise was even more salt in the wound. Naturally, Spock was upset. We've seen Spock have emotional moments when it came to his Captain. "Amok Time" is one great example. After he learns Kirk is "dead", Spock snaps out of the drive that causes Vulcans to DIE unless they screw a woman. He then, understandably, mourns the loss of his friend and prepares to be placed under arrest for killing an officer. When Kirk is shown to be alive, Spock breaks out in a huge grin. Emotionless? Perhaps not.
These are some of the bigger ones I've noticed. I don't count Kirk's revival because it was obviously going to happen, Khan blood or not, and besides, he was only mostly dead. Another is a little confusion since it seemed the Enterprise was going out on her 5 year mission at the end of the 2009 film, but it was obviously a 6 month shakedown cruise/maiden voyage. Get out and show the colors, as it were. The 5 year mission is one for exploring unknown reaches. That said, I'm sure I'll get a few other things pointed out to me. If my Trekkie brain can come up with an explanation, I'll do so. Until then, Live long and prosper.