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".

The universe does not revolve around lazy sysadmins

Using the distro package manager for eggs, gems or jars is an exercise in futility.

Bundler, Maven, NPM et al are not flawless, but maturing rapidly, and a much better fit to the problem domain.

Why must everyone reinvent the wheel, but do so in an incomplete way?

EDIT: I know that's not a satisfying answer. But, as far as I can tell, it is the primary reason that runtimes like Python and Ruby include their own package management rather than falling back on the package management that the OS provides.

Which is why development, QA, staging and production are all separate environments. Do what you want in your dev environment: when the code is ready for testing let the ops team know what the dependencies are. We'll take care of wrapping everything in packages and updating chef/puppet/whatever to deploy it.

And, as a extension of that, if you are using virtualenv+pip for testing, it makes sense for the deployment to use that too, as that means that the testing environment is closer to the deployment environment.