So after reading the white font on STiD, and while still having enjoyed the heck out of the movie, some things rang true for me in the comments.
I've read plenty of fanfic, and some it was truly brilliant in how it dealt with true alternate universes and married them well to canon, complete with callbacks.
So, yes, it could have been done better, and yes, the final part did seem too call-backy and referential and therefore hollow.
I appreciated that we were in a different universe, and that some things could come about again and yet happen differently yet still have echoes of another universe. But yet, it still could have been smarter.
I get why it was called Into Darkness, and I get the complaints that it felt less Star-Treky, and the entire movie was based on "this is shit we should not be doing, because this is not what we're about" and the moral quandaries therein. Which makes me absolutely positive that any subsequent movies will be more about exploration (talk about things that made me verklempt: the captian's code spoken at the end, which is the show's intro monologue).
I was actually upset many times in the beginning about how the characters were going in directions that were morally wrong, and I don't think that it was until this movie that I realized in absolute clarity that this crew, this ship, wasn't military. What with all the battles and fights. I finally fully comprehended that these people were signed up for discovery and science and knowledge and exploration. And that they'd never signed up for battle or violence in a tactical military sense. And in that way, this movie was awesome. (It also made me mad because Kirk was pulling this staff into combat without giving them the choice to get the fuck off the ship, but I suppose he circumvented that by making his away-team the ones supposedly caught up in any potential violence).