As far as I can tell, there are 4 window classes to be concerned with. (Dialogs would be a separate issue.)

EditorWindow
|- PyShellEditorWindow - EW+breakpoints, replaces WE in PyShellFileList
|- OutputWindow - used by Find in Files
   |- PyShell - the visible shell window

PyShellEditorWindow does not override the title methods and is of no concern to us.

If we want the title for all these windows to start with 'Python', we should 'factor' that out and start with it at the beginning of EditorWindow.saved_change_hook (and change other things in EW). Thinking ahead, another possible use for OutputWindow is for containing the result of running an external program on a file. I think that a leading 'Python' would be fine something like
  Python: PyFlakes output for OutputWindow.py

Adding the flexibility of a title parameter to OutputWindow instead of EditorWindow seems about right. If we do that, the override of .short_title for PyShell in the first patch should be removed and the title passed in to the one and only call that creates a PyShell (PyShell.py, 315).

I would like to add some minimal automated tests (maybe in a new test_misc.py file) using either mock classes or unittest.mock (which I have not used yet).