The problem is the distributions packages are often horrendously out of date. I have stopped using them entirely even for things like Numpy and Scipy which I would really rather use them for (as they take a long time to compile and rely on several C libraries and a fortran compiler). It isn't my favorite thing to have my fabric task compile all the dependencies but there isn't really an easy way around it.[1]

In general I think pip has drastically improved my work flow and code structures. For instance: I no longer use submodules for my library code, I pip install the git repositories. Huge improvement, way easier to manage.

[1] Obviously, you can get around it if you do things like copy the virtualenv and fix the paths as in the OPs post. However, I wouldn't call that "easy".