From here on out I will be talking about what the movie did wrong. I am not talking "trekkie" items either, I am talking about basic things that should have been caught by the writers or any science consultants they had. That they weren't indicates lazy writing, bad editing, and a lack of understanding in several subjects. They don't really detract from the movie from a fun point of view, but they do take you out of it if you think about them for a few minutes.
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- Just because it is called "cold fusion" does not mean it has anything to do with freezing things. A cold fusion device would not create "freeze waves". All that the "cold" part implies is that the reaction is started without having to deal with the types of conditions you find inside stars (super high heat and pressure). Cold fusion is pretty well established as impossible in real life, but I'm willing to give a sci-fi movie a pass on that point and assume they figure it out later.
- Freezing the top of a volcano would make the eruption worse, not stop it. Volcanoes erupt because of a huge build up of pressurized liquid rock under the surface. As anyone who has ever shaken a carbonated beverage container can tell you, capping it makes the eventual explosion more violent, not less (unless you arrange a controlled leak, such as popping the cap just slightly so gas can escape). Unless they vented the pressure somewhere else (and maybe that is why they had the enterprise under the ocean, which is never really explained), they have just guaranteed the natives an even worse time in a little while.
- Kahn's plan is very cliche, but it is cliche because it is a workable plan (the one to get the senior staff together, not the one where he puts people in torpedoes). But the horrible, inexcusable incompetence of Starfleet makes the entire situation unrealistic. No one but Kirk in the entirety of Starfleet could see through Kahn's plan, which Kirk figured it out in less than 2 minutes with no prior information or knowledge about the situation. Further, the entire plan hinges on the fact that they apparently wrote in the regulations the exact room in which everyone important was to meet in the event of an attack. This isn't "Kahn figured out where they were", it is "every single person in Starfleet or who has read the starfleet regs knows where they are". At the very least Admiral Marcus should have realized that he was a target and moved the location.
- The most ridiculous thing in the whole movie is the "Transwarp Transporter". Kahn beams from Earth Kronos using a device slightly bigger than a suitcase. From the center of the Federation to the capitol world of a belligerent power. How can they be a threat, if we can just beam explosives at their planet without even taking them out of the factory? Why do we even need starships if we can just beam from planet to planet? Why didn't Admiral Marcus just beam the torpedoes at Kahn instead of sending out the Enterprise?
- Correlated with that is how Kronos is apparently 2 minutes from Earth at warp. How can you have two belligerent powers with capitols 2 minutes apart? Even an hour might have been believable, but having these two worlds this close together makes it completely unbelievable that they have not just gone to war and finished already.
- Neither Starfleet nor the Klingon's appear to have any kind of security sensors or defenses anywhere. No one sees Kahn's flyer, no one detects Kahn beaming to Kronos, the Klingons do not see the enterprise 20 minutes from their capitol, do not notice the shuttle till it is about to land, nor can they track it when it leaves. The secret Jupiter shipyard can't detect a shuttle flying right up to it making no attempt at stealth, no one in a small convoy of ships can see said shuttle just slipping in with them, and at no point while a battle is going on in lunar orbit or during the several minutes it takes the Enterprise and Vengeance to fall through the atmosphere does anyone notice and respond in any way until the Vengeance break the cloud deck. Also, there were several other ship captains and first officers in the meeting earlier; where are all of their ships while this is going on? Where are the orbital defenses around Earth or Kronos?
- Why does McCoy need Kahn alive? He has 72 other augments in stasis, one of whom he later pulls out while keeping him unconscious so he can use the stasis pod he is in. Couldn't he have gotten a blood sample from any of them?
- You would never put a large multilevel vertical atrium on a ship exposed to vacuum. As soon as there was a breach anywhere on the ship, you would expose all of the decks to space.
- We finally get seat belts in Star Trek, and they are really dumb computer controlled seat belts. What happens if something knocks out the computer? Why aren't they worn more often, since we clearly see you getting knocked around in several scenes?
- Why is Carol Marcus in this movie? She doesn't give any exposition that couldn't have been handled by Spock, she gets kidnapped by Admiral Marcus in 5 seconds and then basically ignored. I thought maybe they would set her up for a reverse Women in Refrigerators relationship with Kahn after she saw him kill her father, but she is absent for almost the entire rest of the movie and it is Spock who gets to go after Kahn in a rage.
- Uhura's entire role in the movie is to be in a relationship with Spock. Nothing she does in the entire film has anything to do with anything else.This is a waste of the character.
- Is there no one else working in engineering other than Scotty and his pal? Kirk bypasses the entire existing engineering staff and gives the chief engineer position to Checkov, an ensign whose primary post is tactical. In a real situation, there would be a 3rd officer who would take over from him.
- There was no need to bring in Spock-Prime (Leonard Nemoy). His presence is strictly fan service.
- I'm sorry Zachary Quinto, but you cannot do the Shatner "KHAAAAAAAAAAAAAAN".