1. It was introduced very late, meaning the community had already formed patterns of contribution around a flawed flat system. This is a problem of the flat system, not of the namespaced one.
2. It is still to this day entirely optional (for understandable backward compat. reasons). This gives namespaceless packages a misplaced position of authority over namespaced ones, which erodes the value of namespacing.
These are tough problems to get around if you start with a flat structure, but they really just outline the urgency of switching to namespaces for a relatively young project.