Just did some testing (with two gEdit windows) this morning, Ubuntu
14.04 updated to the latest packages as of today (2014-04-01). I apt-get
installed ubuntu-gnome-desktop and kubuntu-desktop on a regular Ubuntu
14.04 install.

GNOME desktop (gnome-shell): Both gEdit windows can be scrolled with the 
pointer hovering over the window, regardless of focus.
GNOME desktop classic (I guess still gnome shell?): Same as GNOME desktop, 
scrolling works while hovering, regardless of focus.
KDE plasma desktop: gEdit window needs to be focused to be scrolled
Ubuntu Unity desktop: gEdit window needs to be focused to be scrolled

And on Ubuntu 14.04 (around beta 1 packages) on a netbook with a
touchpad and mouse connected: Nautilus windows can be scrolled with the
touchpad while hovering, regardless of focus, but NOT with the mouse.

So, what makes the gnome-shell desktop different to Unity and KDE? The X
server, GTK etc are all the same.

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https://bugs.launchpad.net/bugs/1240957

Title:
  Scrolling behaviour and window focus has changed and is inconsistent

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