The thing is, when it comes to understanding the subtleties and unspoken implications and social cues of other (especially primitive-exotic) cultures she seems to do just fine. It's only in the context that she should understand best that she stumbles. For example, she could write a dissertation about all the intricacies and complexity of the mating rituals of the bushmen of nowhereland Africa, yet in her own life she doesn't understand why using one man for sex and one for intellectual conversation, without bothering to tell either of them what their roles are in her mind, might be offensive to both men.
Also, Booth became a real *ss after Bones got pregnant. I realize he wants to "protect her" (as though she can't do that herself?), but he treats her like some brittle child in some of the more recent episodes. BTFU.