To do a Kirk and Spock are soul mates centric film would be just wrong. Up until the point of Kirk's death scene they didn't even know each other.
I say this because how close could they have been if Spock didn't even know how close Kirk and Pike were. I am sure there were many off shift com calls between the two in Kirk's quarters.
I'm guessing that Spock was not present for these because he was spending his downtime with Uhura. Bones knew how close they were because it was he that spent downtime with Kirk in his quarters.
I am also sensing from the events of the movie that Kirk and Spock did not spend time together playing 3D chess. They do not have appeared to have spent anytime having discussions about life and such while say writing reports because Spock still had no clue about Kirk's style.
I could go on an on in all the ways that TOS and AOS differ with regards to the Kirk/Spock friendship. I know that now that they have had their death scene they are all the sudden best buddies.
I don't believe that. I believe that the dynamics have changes in this verse in that Spock has Uhura and where as in TOS he might have had emotional interactions with Kirk after a mission, he now does so with Uhura.
Furthermore, it is Bones that Kirk was willing to sacrifice everything for when his arm was caught in the missile. He was so upset that even Uhura deigned to comfort him with a hand on the shoulder.
It was only with Pike and Bones that Kirk showed any emotions whatsoever. I am positive that the Kirk/Spock friendship has been altered now that Spock has seen Kirk die.
But it is Bones who is the moral compass of Kirk and it would be him that could get Kirk to focus on what Spock is saying with regards to how to proceed in certain situations.
So IMO you need more Bones so that Kirk will focus more on what Spock and others are saying. Bones knows Kirk like the back of his hand and can handle him better than anyone else.
I think it is a big mistake to ignore the importance of Bones. If they had had more Bones in this movie things would have been very different. I believe Bones would have called Jim out on wanting revenge for Pike's death etc. He could have helped Jim think things through and realized certain truths sooner.
Sorry for the mini rant but I am very passionate in my belief that it is most important to bring Bones back to the inner circle and to actually have some lines written for him that aren't well just plain ridiculous