I don't know about you. A common namespace composed as a tree makes sense to me. Splitting of user data makes sense to me. Splitting data from code executable code make sense to me. Splitting configuration from other data does. So does splitting code into executables and libraries, splitting into per machine/shared, and splitting into core OS and other (now reversed). The actual names don't matter all that much, but they are short and standardized so we use them.

What do you find weird about the directory naming structure?