Lately bought a Thinkpad Yoga and started using gnome3/ gnome-shell because of its nice tablet features. I really have to admit that people were visionary and implemented all this bullshit that only hinders you while working with mouse and keyboard. Good work with this, although I really miss the simple aesthetics of my former XFCE desktop with the BeOS-like window borders overall less clutter and especially superswitcher.
Anyway, now I’m on gnome-shell and had this really annoying bug where you always click “through” full screen windows (like Kodi, mplayer, virt-manager, HTML5 videos etc). Say you just opened kodi, put it into full screen and want to do a right klick — next think you see is the context menu of your desktop – yeah.
Long story short. I switched my mutter window ‘Focus Mode’ from “Mouse” to “Sloppy” using gnome-tweak-tool, section “Windows”. The focus still follows the mouse but clicks into full screen windows stay where they belong.