Based on what I've been told about the comic storyline so far, and things Orci has said, Kirk will do some "growing up" both as a man and as a starship captain in STID.
Orci basically said that Kirk may be the Captain of the Enterprise at the end of ST2009, but in STID he will learn what it means to be the Captain, and will have to make some hard, character defining decisions.
Never keep a Vulcan waiting...
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