Having "Edit in IDLE' work uniformly for all installed versions would be great.

> set the working directory properly

This needs some discussion and coordination.  I am thinking of patching IDLE to switch to $HOME when cwd is the python install dir, but this would very likely only be done for 3.6 as part of re-writing the startup code.

> and any environment variables that may be needed/helpful.
Can't think of anything at the moment, but this has never been an option.

> treating Shift+Click differently from a regular click, if that was any value (run in IDLE and leave the interactive session open, perhaps?).

IDLE's "-r file.py" runs the file and leaves Shell open.  I believe this is meant as a substitute for setting $IDLESTARTUP or $PYTHONSTARTUP and using -s.  For development, one should open in the editor and hit f5.   There might be a controversy whether to run in IDLE or 'python -i'.  If control or alt click could be distinguished, both would be possible.

Are you going to open issues, or should I?