I've done just a small amount of work with node, but as a professional Python dev, I very much agree that package management is one of (if not the most) significant downsides of our ecosystem.

One feature I'd love to have personally is a clear way to manage only direct dependencies, but have reproducible builds in pip. @nvie has done some great work in this space [0][1], but not all of us have caught up yet. :)

0: http://nvie.com/posts/pin-your-packages/

1: http://nvie.com/posts/better-package-management/