The simplest way would be to add an alias to python3 to always point to the native python installed. Add this line to the .bash_profile file in your $HOME directory at the last,

alias python="python3"

Doing so makes the changes to be reflected on every interactive shell opened.

As Inian suggested, you should alias python to point to python 3. It is very easy to do, and very easy to switchback, personally i have an alias setup for p2=python2 and p3=python3 as well to save on keystrokes. Read here for more information: How do I create a Bash alias?

Here is an example of doing so for python:

alias python=python3

Like so:

$ python --version
Python 2.7.6
$ python3 --version
Python 3.4.3
$ alias python=python3
$ python --version
Python 3.4.3

See here for the original: https://askubuntu.com/questions/320996/how-to-make-python-program-command-execute-python-3

You can just specify the python version when running a program:

for python 2:

python filename.py

for python 3:

python3 filename.py