What you're saying makes sense in some cases. In most of the use-cases I've encountered I want to run a separate version of Python than the operating system. This allows me to update Python independently to the OS. I was stuck supporting CentOS5, which ships with Python2.4, long after Python2.7 had shipped. Jumping straight to CentOS6 or 7 introduced quite a few variables (not to mention quite a few bugs in the standard library were patched and it was nice to take advantage of that without upgrading the OS).

It'd be nice of macOS shipped Python 3.