You are using pip3 to install flask-script which is associated with python 3.5. However, you are trying to upgrade pip associated with the python 2.7, try running pip3 install --upgrade pip.
It might be a good idea to take some time and read about virtual environments in Python. It isn’t a best practice to install all of your packages to the base python installation. This would be a good start: http://docs.python-guide.org/en/latest/dev/virtualenvs/