I don't agree that Uhura's expansion in the new movies "over-writes" Bones in the big three. Bones is still Kirk's best friend, and that hasn't changed at all. Any story that involves Kirk heavily will have an important role for Bones. It's just that the NuTrek universe has given Spock
a best friend too (Uhura).
See, I agree. In TOS, the Big three was Spock (Logic), Bones (Humanism/Emotion) and Kirk as a mixture of the 2.
NuTrek puts it at Kirk (Emotion) and Spock (Logic). With Bones being the voice of reason of Kirk's emotions while Uhura is the voice of emotion for Spcok's logic.
This justifies her increased role in the new films easily and the fact that she's a linguist on a mission to an alien planet to catch a terrorist doesn't make matters worse either.