That is an overall net positive, but I still think that, in order to be fully compatible with the ideals of academic freedom and reproducibility, papers should depend largely (ideally, only) on code that is fully open source. I recognize that this may not be compatible with the interests of companies like Wolfram and Math Works, but I think it is in the best long-term interests of research as a whole.
I think so too. Patrick Collison and I and likely many others have ideas for an open source Mathematica competitor in idea stages and design, and in the back of our minds. But it's a herculean task. Maybe one day we will get to it.
It is a Herculean task, but that's part of the miracle and promise of open-source: you don't have to do it alone. To address the lack of a good MATLAB-style science oriented IDE, I started a project (http://github.com/cgranade/scicore) today to try and attract more intelligent coders than myself to help. As others have pointed out, SAGE (http://www.sagemath.org/) is a good effort at an open-source Mathematica competitor, even if I feel it lacks something in the UI department. Point being, it's possible to get a project going that becomes larger than yourself using an open model.
