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I love Python for its simplicity. This doesn't feel simple.
Thinking of unit tests and sphinx from the start is a good idea. But vagrant does seem like overkill for most things given virtualenvs, and that setup.py makes me sad.
Nice idea, but does this offer anything over and above the well-supported and functional pyscaffold? [0]

[0] https://pyscaffold.readthedocs.io/en/v2.5.7/

Well, cookiecutter came first, has a huge library of supported templates, and works across multiple languages.
Any reason why tox isn't included? I find it a lot easier to run tests, especially with different python versions.
This seems like a good place to get inspiration from, or quickly look up file formats and conventions - but actually using it? That would be an overkill.

(This template, alone, is 1000 lines long, counted with wc -l. The last Python project I released was 500 lines long, including setup.py and README.)