The story structure is that of How James Kirk Became Captain of the Enterprise. The emotional structure is Spock's story through and through. This mismatch was very awkward.
How did you reach this conclusion? I'm honestly asking because I don't feel it was at all about James becoming Captain. It happens yes, but at no point is the conflict of the story centered around Kirk's ass landing in that chair. Star Trek 2009, for me, falls into (though not evenly) the "Event" mold of Orson Scott Card's MICE quotient.
"In the Event story, something is wrong in the fabric of the universe; the world is out of order. In the ancient tradition of the Romance (as opposed to the modern publishing category), this can include the appearance of a monster (as in Beowulf), the unnatural murder of a king by his brother (as in Hamlet), or the reappearance of a powerful ancient adversary who was thought to be dead (as in The Lord of the Rings). In all cases, the "golden age" has been disrupted, and the world is in a state of flux."
The "something" that's wrong in Trek 2009 is the appearance of Nero. He is literally what's wrong in the fabric of the universe. He has traveled through a hole in it and kills Kirk's father immediately after. This is the conflict that demands resolution, not Kirk's lack of rank. The succeeding scenes are driven by the danger Nero poses to Federation Space (He destroys Vulcan, threatens Earth) and, again, not by Kirk's rise to the rank of Captain.
"The Event story ends at the point where a new order is established, or the old order is restored."
Order is restored when Nero is driven back into the [black] hole he crawled out of and the crew of the Enterprise find themselves where they should have been had he never appeared. Or, more specifically, the negative effects of Nero's appearance on Kirk's upbringing subside as he and Spock find a harmony within their conflicting ideologies.
For the "emotional structure" of the story I must again refer to Mr. Card and ask: "Who hurts the most?" For you, obviously, the answer is Spock. However, for others (myself) the answer is also Kirk. It is true that the destruction of Vulcan was a heavy blow and a painful one for Spock to endure, but Kirk lost something long before Nero lowered that drill into Vulcan's atmosphere. Too few scenes deal with this, but there are those few that do. The scene between Kirk and Pike in the bar does this. Kirk harbors contempt for the absence of his father and those that revere him. This makes him a bit less approachable than TOS Kirk and rightfully so, but calling him a dick is a bit much. His disdain for his father's self sacrifice is evident in the trial just after Kirk states "I don't believe in no-win scenarios." This contempt, however, does not prevent him from giving Pike and others the respect they deserve. And as we all know, you have to give respect to receive it.
So, for me, this depicts Kirk as both sympathetic and respectful which invalidates:
He engenders no emotional identification, no respect
As far as Kirk's "arbitrary" promotion is concerned, it's not the most unheard of thing in the history Star Trek. Many Captains were lost in the attack on Vulcan and field promotions don't have to conform to time/grade requirements, nor involve committees or promotion boards. The Captain is an anchor (as Diane Carey describes the position in "Best Destiny") and besides Spock (Which was his first choice), Pike didn't have very many "Anchors" to choose from. He did the best with what he had and it just so happened that it was the correct choice. One that saved his life and billions more.
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