Early Episodes and more recent Episodes

I think it is more just a change in the writing then any planned thing from conflict between Cam and Brennan or any psychology reason. The 1st season boss was not in quite the same profession, he was more of a history type and cultural type than a flesh and bones scientist. So the early Brennan was the only one to do both jobs and then they decided to write it so that she would be the bones person to fit the title and bring in a new boss to do the flesh.

Hmmm. Well, I think it's the introduction of Cam, honestly. Before Cam, there was no one else to do flesh, so she did that too. Technically, a forensic anthropologist DOES work with flesh when they need to. They're called in when a body is too badly decomposed to use other methods of identification. Very rarely does this mean the body is COMPLETELY skeletonized. Instead, there's a one to two week period where all the flesh is methodically removed so as not to harm the bones, which are later examined. Before Cam, there was no character to look at flesh. With Cam, came the introduction of a forensic pathologist, who could gather information from the little remaining flesh. Brennan, wants the flesh removed to get to the bones, so sees little worth in it, whereas Cam specializes in gaining information from it. That's why in later episodes Cam looks at flesh before it's removed.