There are also problems that aren't directly related to the raws. As a result of this, more realistic raws won't necessarily result in more realistic combat (yet).
For instance, there's no way to make ribs consistently get in the way of organ blows without results like you see in my signature, since the ribs are checked independently.
Also, I'm not sure if I've mentioned this before, but it seems like all blows against a body in DF are treated as if that body is held perfectly still, or against a wall or something. In real life, if you punch someone in the arm, much of that force just moves the arm out of the way, whereas if the arm is held in place, you're much likelier to break it. It's like every time you kick someone in the head in DF, you're curbstomping them, or kicking them against a wall or something. This is only a suspicion on my part, but it would explain some things.
Also, I believe one reason skulls break so easily is because certain things aren't factored in at all, such as the shape of the skull contributing to its durability, or the bone structure of the skull possibly differing from most other bones.
That leads me to another comment which I'm not sure has been addressed yet: It seems like heads in DF have fairly normal tissue layer relative thickness, comparable to either arms or torsos (I forget). As a result, a fat guy in DF has a whole lot of fat over his skull, and same with strong guys and muscle. This is a little silly!