I'm not sold on the utility of a notes-as-a-graph view, but expanding on #3 (tiled view of open notes), and the ideas put forward in Andy Matuschak's Peripheral Vision note, might it be possible to have a single note as the 'centrepiece', with notes it links to dynamically displayed around it's edges. This could allow for 'dismissal', or for 'following the chain of ideas'
Could one perhaps split the viewpane in order to follow multiple paths through a chain of ideas?
I like that - or possibly spawn a whole new (terminology not-yet-defined) pane/buffer/view/tab.
Possibly keep a graph-based history of traversal also?