It's easier to teach someone to write some Python and use a Git GUI than it is to teach a new student (who is not a programmer) how to properly use Mathematica with version control. Notebooks are, by design, made to be interactive and promote an incremental, playful discovery process. That is intuitive and students pick it up very quickly.
This means that code is passed around as (in my experience) bloated, poorly written, poorly documented and inefficient (no FP, all imperative) notebooks containing multiple "orphan" sections which were just quick hacks to try and see if something worked. Of course you can learn to write packages and good documentation which integrates flawlessly in the documentation center, but that takes time and effort most scientists would not be willing to give.
It is possible to write notebooks directly in a text editor and then have them run. That just gave me an idea for a weekend project...
Update: I guess I owe the Wolfram Language another look.
https://reference.wolfram.com/language/tutorial/UsingATextBa...
https://reference.wolfram.com/language/tutorial/WolframLangu...
I like the playful-discovery process concepts but the difficulty in versioning and sharing seems like a fascinating UX challenge that comes along with it... so I'd be deeply interested in any ideas you might have on that what influences that balance (positively or negatively) :)
See http://arxiv.org/abs/quant-ph/0206089
Also funny, from the same author:
> “The impact of NKS on all the areas of computer science and physics I’m familiar with has been basically zero,” he says. “As far as I can tell, the main impact is that people now sometimes use the adjective ‘Wolframian’ to describe breathtaking claims for the trivial or well-known.” [Martin] Davis offers a sunnier take: “The book has a lot of beautiful pictures.”
https://en.wikipedia.org/wiki/De_revolutionibus_orbium_coele...
I have found that pretty much all of what Wolfram writes is closer to this article than the popular internet opinion. I suspect that that's because his tools scratch his intellectual curiosity...they exist so that he can start with the sort of math that starts this article and go from there...or write a book like A New Kind of Science.