In case some of you are interested: yesterday I updated Penelope (now it is at v3.0.0), with a complete code refactoring, new options, MOBI output, and a more rational command line interface. Get it from:
https://github.com/pettarin/penelope
EDIT: Penelope v3.0.1 is now available on PyPI (so you can install it with: $ [sudo] pip install penelope) too!
https://pypi.python.org/pypi/penelope/