Also, we normally set ".py", and ".pyw" into the PATHEXT environment variable, so that a script "pysetup.py" can be invoked from the command-line as just "pysetup" without the suffix. This gives the same experience as using a "pysetup.bat".

I would say that pysetup seems a little more polished (and shorter) than the -m form, especially for users new to packaging. After that, I agree with Paul's ordering of .exe, with the setup script having to be named pysetup-script.py if we use the "standard" mechanism, or else if we use a custom .exe, it can of course be called whatever we want.