This seems to have previously been a problem starting in 15.10, and after upgrading to Ubuntu GNOME 16.04 the problem is still not solved. Click to focus specifically seems to be bugged on GNOME applications. I can get the windows to be active by clicking on the title bar, but I cannot simply click anywhere in the window.
I can "work around" this issue by changing the raise behavior to "sloppy" or "mouse" but those solutions do not work for me because I constantly move the mouse to the side of a window or work with windows on top of one another and sloppy and mouse constantly do what I do not want them to do, which is raise a window and make it active by having my mouse over it.
More than not being raised, they also seem to not really be "active", as trying to type in those windows results in the input being in the raised window. I can drag and drop a file/icon into a nautilus window and it works, but if I select files with my mouse and try to ctrl+v them, they will not be copied.