Two negative factors.

1. Users may edit the user config files 'by hand'. They occasionally must edit them to fix problems. Burying them in a *hidden* directory (invisible in Explorer) will make editing much harder, *especially for beginners*.  Even as a long-time Windows user, I only recently learned how to access %APPDATA% in Win 7, by fiddling with the entry bar the right way and adding exactly 'AppDate\' to the existing path, displayed as a path.  I am pretty sure this is different than with XP.  I imagine this has changed again in Win 8 and Win 10.  I really do not want to have to explain the Win version specific details when someone asks how to fix a problem here, python-list, or stackoverflow.  I doubt either of you want to either.

2. The one .idlerc directory is used for all currently installed python versions.  When one installs a new version, such as the upcoming 3.5.0, the custom font and size, custom keybindings, and anything else, are just there.  We cannot magically go back and change all existing installations.