Default to python3 for '/usr/bin/env python'

That's because env is searching python in your PATH, not on any shell builtin, or alias or function. As you have defined python as python3 as an alias, env won't find it, it will search through PATH and will resolve python to /usr/bin/python (which is python2).

You can check all the available locations of executable python, in bash, do:

type -a python

You are out of luck if you want to use an alias in shebang as by definition, shebang needs to be an full path to the interpreter executable, which the env should resolve python to when you use /usr/bin/env python. To interpret the script using python3 use the shebang:

#!/usr/bin/env python3

Given the number of script which call /usr/bin/env python expecting python 2, it's probably a bad idea to have python actually be python 3.

As Benny said in a comment, /usr/bin/env python3 is the right solution.

I found a better solution than those posted here: http://redsymbol.net/articles/env-and-python-scripts-version/

The basic idea is to put a symlink name python to python3 in some other smartly named directory and then put that directory in the beginning of $PATH so it gets found before the one at /usr/bin.

So:

mkdir ~/bin/env_python3/
ln -s /usr/bin/python3 ~/bin/env_python3/python
$PATH = ~/bin/env_python3/:$PATH ./script.py

Using this solution you don't symlink /usr/bin/python to python3 and break scripts that assume it is python 2 and you also don't have to edit the script that you downloaded from someone else.