Well, personally I'm not moaning and griping for the sake of it. I enjoyed the movie but I also really enjoy poking fun at the silliness of it all.
And part of the problem with what we see on screen is that it leads us to the conclusion that maybe Kirk is not as fit for command as Pike seems to think he is - it really smacks of that episode of the Simpsons where Homer is put in charge of the submarine because the captain likes the cut of his jib and that was hilarious. He succeeds because the writers want him to, not because of any great aptitude.
And I really don't see any way to rationalise or improve upon Kirk stumbling across Spock in a cave. There are so many things wrong with that scenario not even the Universe can fix it
Even so, coming back to the comics, aside from some of the silliness that was already present in the original episodes, they are keeping the characters on a relatively even keel so far.