Edited to add right up front: This is probably a post that's going to get a lot of TLDR (too long, didn't read) replies. Oh well, felt good to vent.
Matt Singer quotes Khan:
He used my friends to control me; I tried to smuggle them to safety in the very weapons I had designed. But I was discovered. I had no choice but to escape alone. And when I did, I had every reason to suspect that Marcus had killed every single one of the people I hold most dear. So I responded in kind.
Singer himself says about this, "But as far as I can tell, neither Marcus nor Khan know Khan's crew are inside the torpedoes when they are given to Kirk. So, Khan's whole plan was revenge for the murder of people who hadn't been killed, and Marcus' whole plan was to give Khan the one thing he wants. None of it holds up to scrutiny, and all of it is unclear."
What? Khan's quote is very clear. Khan put his people in the torpedoes. He may be masking his real motive for doing it, but he admits he did it. He says he was discovered. That had to be by Section 31, which would mean Marcus knows. So, found out, Khan has to save himself. He logically assumes that when Marcus gets ahold of the seventy-two torpedoes, he'll summarily kill Khan's crew to cover things up. Instead, Marcus doesn't, maybe deciding they're more useful as bargaining chips to get Khan back or for some other purpose, later.
But Khan, in a fit of emotional rage fearing Marcus did kill them, goes very rogue and very public, and now Marcus must get rid of them. Whether it's the best way to do it or not may be arguable, he takes advantage of Kirk's willingness to go after Khan to get rid of the torpedoes more or less in plain sight. When Khan realizes Kirk has exactly 72 torpedoes, it occurs to him his people may still be inside and alive. The story could've been very different if Khan had been told there were 28 or 8 or 12, or 142 torpedoes. Seventy-two was the magic number.
What in the world about that is unclear or doesn't hold up to scrutiny?
As far as contemplating Kirk's ups and downs in rank goes, WTF? They take the Enterprise from Kirk at a meeting where Pike wasn't there to defend him. After a short cooling off period, Pike talks to Marcus, and in a great selling job, talks Marcus into letting him essentially take Kirk under his wing (let's face it, even Marcus would have to admit Kirk is exceptional). Also, Pike may have influence over Marcus that comes from them having a sort of mentor-protégé relationship, or at least Marcus greatly admires Pike and what he thinks (Marcus telling Kirk he talked Pike into jointing Starfleet insinuates that). Then, Pike is killed, and Marcus lets Kirk captain the Enterprise again because under the circumstances he thinks, "What the hell, he'll either be my scapegoat for war or get himself killed, anyway."
As far as the, "Oh, shit," moments go. I thought most good action movies will full of quite a few of those.
As far as Kirk being alive ten minutes after he's dead goes (movie time), so what? Spock was probably dead ten minutes on the Genesis planet before coming back to life. The only difference between his "death" and Kirk's was the time in between the movies for Spock.
Here's the most inane and ego-involved line from Singer's piece, "
Star Trek into Darkness isn't as great as its reviews suggest -- or as bad as its backlash." There were 215 positive reviews out of 247 reported on RT. What percentage of those reviewers have recanted their positive reviews a year later? Has the backlash on Youtube completely enveloped and negated all those positive reviews? Which by implication were all knee-jerk reactions to the movie, by the way. They were just unthinking tools, too unsophisticated to ask the right questions and be intellectually honest with themselves about how bad the movie really was. All 215 of them.
The last part of his article is full of holes, too. For all we know, some medical branch of Section 31, or maybe even some mainstream Starfleet medical personnel have been or are studying Khan's blood for its restorative qualities. However, after the 1990s, as brought out on DS9, eugenics is an ethical third rail for humans. One shouldn't expect Khan's blood to be as common as flu shots.
As far as using blood from any of the other 72 go, how does one know all 72 in the tubes are supermen (or superwomen)? What if only ten are? Or one in five? Or, even zero? McCoy knows for certain about Khan's blood. Is McCoy feeling lucky? Pick a tube, any tube.
Singer says the movie is cynical. Gee, after seeing this country rationalize going after the wrong people (Iraq) after 9/11, maybe we're entitled to be cynical about our leaders and their motives. The ending of STID is positive and optimistic because it looks as if after their bad moment, the fever is broken. The war lust is gone. Marcus and all his ilk are just as responsible for the Vengeance crashing into San Francisco as Khan was, because they created and perpetuated the atmosphere that led to it all. By the end of the movie the evil has been exposed, and the demons seem to have been purged. Why not be sincerely hopeful at the end of the movie?