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I've been using Idle to teach beginning programming to university
students for the last 6 or 7 years. I've taught hundreds and hundreds of
students, and the single biggest confusion with Idle is this:
"New Window" in the file menu is ambiguous
Proposed fix: change "New Window" to "New File", or "New Program"
Many beginners don't get the difference between a shell window and
program window. I spend some time explaining the difference, and yet
they see "New Window" and don't know if this means a shell window or
program window.
Obviously this is not an issue for non-beginners, or even for anyone
willing to experiment for a minute or two, but it seems to me this is a
small change that could be useful to beginners. 
Plus more precise menu options are usually a good thing in general.