Question: Why does Khan have to be alive for McCoy to use his blood to save Kirk? The blood will be removed from its supply anyway when drawn.
Chosen answer: McCoy has no real idea how much blood he's going to need to bring Kirk back - given the catastrophic radiation damage to his body, there's every possibility that he might need multiple transfusions over a period of time, which would be much easier if Khan was still alive. Plus there's also the issue that killing Khan could well involve spilling some of the blood that McCoy so desperately needs. Bringing Khan in alive is the best way to maximise their chances.
Question: When The Enterprise reaches Kronos, we see one of Krono's moons was half blown away long before the events of Into Darkness Take Place. In Star Trek VI: The Undiscovered Country, one of Kronos' moons blows half away in an "incident." That incident takes place later on in the lives of the characters when they come close to retirement in the previous reality before it was altered. Are we to assume that either: A different Kronos moon blew long before Star Trek VI in a similar fashion, or that the change of events from the previous film had such a strong butterfly effect that the Kronos moon suffered an incident much sooner than it originally had?
Chosen answer: The explosion of the Moon Praxis in the original Universe was due to extensive over mining and energy production. In the first movie that took place in the alternate reality, an entire Klingon armada was destroyed by the Narada. It is logical to assume that the Klingons began to over-mine the moon in order to obtain the resources necessary to replace so many lost ships, causing the moon to explode several decades before it happened in the Prime timeline.
Question: What happened to all of the Enterprise's Shuttles and the ship Kirk's team took to Qo'nos? Did they all become disabled that only Kirk and Khan would jump out an airlock and shoot through a dangerous debris field to board the Vengeance? Rather than taking an entire strike team to take out the minimal crew on the other ship, just the two of them go. Makes no sense, given the situation. Also, consider that even the escape pods have propulsion capabilities as shown in the previous movie when they ejected Kirk off the ship.
Answer: The plan is for Kirk and Khan to sneak aboard the Vengeance, with Scottie's help, without being detected. That could not be accomplished if they took a shuttle or used an escape pod. It would have been spotted, and it would be impossible to land a shuttle on board without the bridge crew knowing it. Even though there is a minimal crew on board Vengeance, they could ambush intruders as they exited their craft.
Question: With all of the Federation's extraordinarily advanced knowledge, science, medicine and technology, why is it that they can't seem to repair Captain Pike's physical injuries? In the original series, Pike was crippled and hideously disfigured by Delta Rays; but the best they could offer him was a motorized wheelchair with a couple of "yes" or "no" flashing communication lights. In the rebooted franchise, Pike suffered much less severe injuries; yet, once more, all they could offer him was a simple wheelchair in the first movie, and then a walking cane in the second. In Star Trek canon, we know that they have performed brain and spinal transplants, regenerated damaged organs, healed mortal wounds (in a matter of seconds), cured horrible diseases with a single hypo-injection, and even resuscitated the dead on more than one occasion. In Star Trek novels, there is mentioned even the possibility of cycling an injured individual through a previously-stored Transporter Pattern and completely removing injuries altogether. Yet the best they ever did for Captain Christopher Pike onscreen was a wheelchair and a cane?
Chosen answer: Captain Pike was tortured by Nero, a Romulan from the future. Surely when it comes to torture they know how they can inflict the maximum amount of pain, and also permanently injure someone. Or else nobody would be worried about being tortured. Nero also used future technology to do this, using methods nobody could cure at that time.
Answer: Unless the cold fusion went directly into the volcano, all the way to the source of the pressure.