The decision in Gnome to move buttons in dialogs to the headerbar is driving me crazy! Why would they do something like that when they don't control the button placement within applications like Firefox, Chrome, Inkscape, GIMP, ...
Also every single OS I can think of, Commodore 64, Amiga, Windows, OSX, iOS, Android, Blackberry, Meego, WebOS not to mention all websites on the entire web, puts buttons in the lower right corner.
This is also where your eye moves when reading a book. Maybe if I was a 100% Gnome user this wouldn't be an issue, but I use Mac/Windows for work and got an Android phone in my pocket.
You might think "that's not worth losing your faith over", but it's not just that. Of the top of my mind: the removal of the desktop icons, the removal of the tray icons and of course the dialog buttons.
I'm so sad to see them doing stuff like this with thinking it through.