Maybe because of the negative sentiment/bad taste statements like "What's wrong with..." leave. It could say "What can be improved with ... in 2020" instead. Probably not intention of the author but it comes as non-constructive crtiticism/"not recommended to use" a bit too much. Some observations seem to not be directly related to notebooks per se. Other feel like could be made as just entries in a FAQ/best practices section of documentation.
Kudos for looking at real people's work and surveying it.
I wonder how much workflow could be improved if researchers would be temporarily paired with developers - who are generally better at modularising and removing friction in their work.
Personally I believe that a bit of clean-code discipline and following known best practices could solve couple of those pain points.
It's also true some could be improved by rethinking how notebooks work; ie. being able to specify input/output of notebook so it can be used as a library; detaching runtime data from the code so it plays better with version control/publishing; maybe even more radical ideas like adding visual/flow view that helps with linking elements; adding built-in excel-like sheets that can be queried/manipulated could also be interesting; built-in, first class support for relational database (sqlite) could also be a big win.
There are many interesting developments happening in this space and there seem to be some unexplored ideas waiting to be tested out.
