Advantages:

• During typical usage graph is not consulted that often, while
  • current "text"/"dependencies" tabs take consume editor space
  • it's annoying when you click on dependencies by mistake and have to wait
• Having separate toolwindow could perhaps allow graph building in background:
  • when toolwindow is launched, show a progress dialog which can be backgrounded (or canceled)
  • when backgrounded, model can still be built (perhaps using IDEA thread pool to benefit from concurrent model building (task per file)?)
  • perhaps yFiles also allows to generate the view in background
  • when everything is done and finished, show/focus the toolwindow
  • while this will not fix graph building performance for large models it will at least allow the users to do something in the meantime (instead of blocking totally)
• Having bean graph separated from current file would also make sense from logical point of view:
  • Graph toolwindow could have "fileset" combo box to select the fileset to view (instead of being limited to current fileset like it is now)

I assume spring xml editor could have "Open in...bean graph" option to access the toolwindow. In addition user could open it explicitly.
Perhaps it could be a floating window similar to Dependency matrix, with the old "mini-graph" as a navigation aid?