There are no words for how hard you suck.
I disagree with that assessment of Khan. He IS evil and a genocidal maniac. He worked with Kirk to stop a guy who was bent on killing him and his people. He flat out admitted to Spock, once he no longer needed their aid, that he intended to carry on with the agenda that had him and his people sentenced to death in the first place. Kirk and Khan were using one another, and there was no true accord between them, as Spock pointed out with his rejoinder to Kirk's "enemy of my enemy" aphorism. As for "needing" the bad guy alive at the end, that was a crock, and cheapened their "good guy" credentials. They should keep him alive, merely because it's wrong to kill him, just as it would have been when they changed their minds about using the torpedoes on him in the first place. By giving the crew a selfish motive to do the right thing, the writers cheapen the moral stance. The real issue should have been the increased difficulty of Spock's task, because he WAS justified in killing him in that situation.
Wrath of Khan is the high point of the entire franchise, as far as I am concerned, and the two subsequent films are elevated by being considered a trilogy with that one. And I loved the homage and the new twist. The important thing was not that it was Spock who dies, but that the relationship between the two was serviced. In the original, it was about setting up Spock's unselfish character, to appreciate his heroism and mourn the loss of this great guy. In this, it was about Kirk paying tribute to his friend, in spite of his on-going mockery, by acting according to the principles Spock espoused. And using Kirk's death to break Spock's cast-iron control was also very good and true to the character. It was things like that which usually gave old school Spock opportunities to emote to that degree.

And by bringing back Nimoy to discuss his experience with Khan in the original series, they did the best thing they could do by acknowledging the reality of his experience. This was not replacing the "Wrath of Khan" it was simply a different way the same people played out similar scenarios. By having Nimoy-Spock discuss the events of that film, they are not saying "No, no. Here's how it REALLY happened..." instead, they are saying "no matter how he comes at them, Kirk and Spock WILL beat him, and they WILL do what ever they have to in order to do it, no matter the personal cost. By having Kirk sacrifice his life instead of Spock, they prove that the friendship is a two-way street, and it is a friendship of equals, in addition to the justification of Kirk's own commitment. From a narrative/characterization standpoint, Shatner-Kirk, by the time Khan came back, had proven his heroism and personal commitment and willingness to put his life on the line. His heroism was well established. Pine-Kirk needed to prove he was more than a smart-ass with super-competent buddies whose lives he was willing to risk for his own glory, just as Nimoy-Spock had needed to demonstrate that he was more than just a sidekick. Also, there was the vendetta between Kirk and Khan, where Khan proved his worth as an adversary by taking away the worst thing possible from Kirk. He was barely aware of his son, but his life-long best friend was a whole other ball of wax.

To make a long point short, Spock dying was right for the original film, and Kirk taking the bullet was right for this one, and by bringing back Nimoy to affirm that BOTH stories happened, AND coexisted with one another, they managed to pay homage to the original in the best way possible, while taking advantage of the filmmaking technology and youthful actors to tell a more fast-paced and action-oriented story.

I think that by making these films an alternate timeline, rather than a prequel franchise, they are only enhancing the luster of the whole crew, by implying that this is a band of destined heroes, who would be badass no matter what, and whose teaming up is an epic deal, rather than just the guys who happened to be there that time. By having time travelers screw with what happened, they are saying, "No matter what, Kirk & Spock and company would have been heroes by nature. Their friendship & exploits are not just a bunch of guys who became buddies because they shared experiences, they are a group of people who were great because that's who they are, and who stayed together longer than any warship crew should have, because they were a natural team-up and their characters and personalities clicked THAT naturally, that they come together in any timeline. If any of them were boinking in more than one timeline, we'd call it soulmates or destiny or some other super-romantic label. It's all that, but platonic, in the sense of "the highest possible form."

Maybe, but I thought it was obvious. As soon as Kirk went into the chamber, I knew they were going to use Khan's blood to cure him. Not that they needed Khan, they had 72 more like him. That's why it was annoying that they were insisting on saving Khan for that reason alone. And what happened to the guy who was in the cryotube that they used for Kirk? And then put Khan in at the end? Did they just toss his body into space and pretend ignorance?