Windows 8 suffers particularly strongly from this because it's got a lot of software that wasn't originally designed for the Metro style. Outlook (http://i.imgur.com/7fWEmvm.png) is one of the worst examples.
There are so many small things that would help give a hierarchy to the design, like using a darker shade of gray in the ribbon background and maybe the sidebar. Without visual cues it's a mess that you have to stare at to understand.