I use two monitors for my daily work. 
I have a few workspaces setup: 
1. Messaging (IM on monitor one, Mail on monitor two).
2. Web + development (Web monitor one, Terminals for doing web development monitor two).
3. Client apps development (Client apps/VNC/Virtualbox + Terminals related to this).
As you see I have one primary monitor and on the second one I always have related windows. 

According to the design of gnome-shell ( https://live.gnome.org/GnomeShell/DesignerPlayground/MultipleMonitors ) there are two-cases to be supported in the multi-monitor case, linked and unlinked monitors. I clearly uses the linked monitors workflow as described in the document. The current implementation seems to only handle the unlinked case where the secondary monitor is fixed, breaking all workflows related to the linked monitor use cases (like the one described in comment #4 above). 

My first reaction to this new behavior in gnome-shell was that it was a bug with my nvidia driver reporting my monitors wrong. I sent a mail to the developer (since bugzilla was down), to report this, when I was informed that it is supposed to work that way. 
Currently I was forced to revert to an older gnome-shell since that handled the monitors as one single workspace. I can live with all other multiscreen issues, but the basic workflows where I can use both screens must work.

I really hope that the link/unlink option will be treated as a blocker, since I'm hardly that unique with my dualscreen workflows.