I am a research hydraulic engineer at the US Army Engineer Research & Development Center (ERDC) and one of the developers of Proteus, a Python toolkit for computational methods and simulation. I've been working in the area of numerical methods for partial differential equations and high performance computing since 1995.
In the interest of contributing to the roundtable discussion in a timely manner, I'm going to basically post what I put on the sage-support list. I have learned a lot since that post, and I see a lot of good ideas in what others have shared about their knowledge of linux packaging systems like Nix and gentoo.
One area where I have a slightly different opinion is that I think we should focus on just the needs of the Python environment on HPC systems. That includes the difficulties of working with many other packages and system libraries, but I am looking for an evolutionary step in what we currently have working for our Python software. If the resulting python distribution solves the more general problem then so be it.
The way I see forward (from sage-support)
Here's what I think we need: