One of the most noticably broken parts of Gnome Shell for me is that my Pidgin notifications/alerts seem to be broken. They neither flash the item in the taskbar, nor give me a popup to let me know that a new message has arrived. I had an extension to fix this, but that has since broken upon Gnome version change. There is a messenger integration into the user account menu in the top right, but there is no way of changing the client from the default to Pidgin.
I only use Gnome on my travel laptop, so I get little snapshot peeks at how it's going. I've had these problems I've mentioned for quite a while now (and many more besides), it only seems to be getting worse. The Gnome devs seem to be completely ignoring the community and charging off down their own path of weird unusability.
For my main desktop I just run AwesomeWM, which is almost completely pain-free and gets the hell out of my way.
I can't live without the Super+[1,2,3,4...] shortcuts.