For most systems, if you have a "system python" you'll want the system package manager to manage that python (and python packages). Because breaking python can mean breaking the package manager.
Personally I enjoy having a few bits installed under ~/opt/py-venv and simply add ~/opt/py-ven/bin to my path. It's usually no need to activate a venv to use it -- just call that venv/bin/{python|pip|hg|ipython|<whatever>}.
In other words, whenever I "pip install something" that something is installed in my "default" virtualenv. And if/when things get out of hand/I need to upgrade to a new python -- I can just recreate the virtualenv and install whatever is needed.