So when you're introducing a younger, greener Kirk to modern audiences, those are the character traits you're going want to emphasise. Because that's what we expect of Kirk.
(As opposed to a "stack of books" who has never, ever appeared on screen.)
As for his academy days, Kirk said to McCoy in "Shore Leave" that he was so serious at the academy that it made him a target for an upper classman named Finnegan. And he got to finally do what he wanted to do at the academy in this episode - beat up Finnegan.
The "stack of books" from "Where No Man Has Gone Before" is actually when
Lieutenant Kirk was teaching at the academy.
As to reinforcing his "stack of books" line - there were several episodes where Kirk goes, "yes so-and-so were required reading at the academy" and a few where he suggests a solution to Spock/Scotty with "isn't there a theory that...".
The younger TOS Kirk would have probably been more of a serious book-knowledge/resourceful type that picked up his daredevil/real-world knowledge and character traits from his mentors and heroes (Captains Garrovick and Garth) as he worked his way up through the ranks and distinguished himself, IMHO.
As to the JJ-Kirk, it's only been one movie. His character had apparently a different upbringing and different mentor helping him into the academy. His character still has time to mature. Look at Craig's Bond character - very rough around the edges in the beginning and he doesn't become 007 until the end of the second movie.