While Uhura has likely replaced Bones they haven't allowed her character to be a pole of debate, discussion, or dissent like DeForest Kelly's Bones was. The films have her being either too lovey dovey, frustrated, or mad with Spock instead.
Like I said in another thread Bones "emotional" presence of the original has been replaced by Uhura's love for Spock and any debates McCoy might of had with Spock has been replaced with Kirk debating & arguing with Spock instead.
It's not necessarily a bad change per say except my own bias speaking, I love Bones and what he brought to the original show so I do miss that in the movie (not to mention it seems a waste of Karl Urban who is so excellent in the role).
Most of us probably expected McCoy to have equal footing with Kirk and Spock in the 2009 movie, though even he hadn't reached parity in the first season of TOS either. (He didn't even appear in ERRAND OF MERCY. He also has a vanishing act in DOOMSDAY MACHINE's second half.
McCoy's role grew in importance as the show went on. He only joined the main credits in the 2nd season.
Although despite being missing from Errand of Mercy, even in the first season McCoy felt like an important character. Obviously I am not really sure how they decided that McCoy would be part of the main team but it seems like a natural progression not that his role suddenly got so much bigger. It just felt like they put in writing what was already there from the start.