Thanks for working on this Fred, and thanks for the great post about it with all the screenshots. I really like the messaging and user menus. I also like the crumb trail and the thing I like most is getting rid of the settings/navigation blocks.
I also really like having a separate page for settings (instead of shoving them in the navigation).
Without thinking too hard about the code - perhaps one way to tackle this in core would be to have some kind of block region that gets different renderers so it produces menus instead of blocks and then just move the settings and navigation blocks into it.
I don't necessarily agree that everything should move to a 2 column layout, or that the course menu should go next to the course title (IMO it should be next to the user and messaging menus).