It seems like this is where everyone settled and is a good solution:
Virtualenv + pip for development
system wide (apt, dpkg) python etc for system tools and packages.
This makes sense to me. Keep your personal code sandboxed from your system tools.
As an aside, I know there are quite a few tools and programs in both Debian and Ubuntu written in Python. I wonder if we'll look back in 5-10 years and realize/think this was a mistake. Particularly for UI code. I love me some Python, but I cringe every time I have to interact with a Python GUI application.