Beautiful design, horrible UX. (I know, I know. Suddenly everyone on HN is a UX designer. But hear me out.) I count eight distinct types of system font in there, all denoting different data/functionality. Semiotically there are no signifiers other than the size, weight and position of the text. It's the closest thing you can get to mystery meat navigation whilst still providing words. Look at current incarnations of…
I count two typefaces, at varying sizes & emphasis, according to their importance. The header hierarchy and sizing is quite nice actually.
Separating lines are not the only way to achieve grouping or separation, whitespace can be just as (usually more) effective. You can see in the Skype window that a slightly darker background helps isolate the action area and give focus to the chat area. The gestalt principles are also in effect here.
My main criticism would be the unnecessary whitespace at the top of the Explorer and Skype windows, which is also inconsistent with the browser window behind, and causes the window controls (max/min/close) to be too far from the edge and consequently less easy targets. In Skype it's even worse since they are shunned onto the middle of the window. That is an usability nightmare.
I agree with the out-of-focus effect. Maybe the effect could only apply to overlapping windows, if windows are not touching then both are in focus - that solves the multi-app workspace case. OSX uses very broad shadows to basically achieve the same.