Another complaint I have with jupyter notebooks is that they don't play nice with git. For this (and other reasons), I much prefer Emacs org-mode, or even running Python in Rmarkdown+Rstudio+reticulate.
I second emacs-org mode. It is extremely powerful though I don't know if it addresses GPs concerns. You could just execute the compiler etc against the actual program from within the code block and then "+CALL" in other sections to avoid the copypasta'ing I guess. I don't do very advanced stuff so I haven't run into problems with just using code in the blocks.
The main problem with emacs org-mode is that users probably need to use emacs, and lots of people have their own editor preferences, and while some have org-mode-alike's, they aren't as fully capable as emacs org-mode. Which is what Jupyter addresses by making the interface more accessible/editable to all.
That said, I think one of the most important factors that the linear notebook flow encourages is a focus on reproducibility, whether it's Jupyter or Org-Mode. I feel like overcomplicating the dev environment would make the much harder and would at least need to be planned for.
Jupytext solves this for me completely. It is an extension to jupyter code which can be turned on (globally or per-notebook, with additional configuration options) which automatically syncs the notebook to a file which can be checked into git and has nice diffs. It is a two-way binding, so editing the file will include those changes in jupyter, and if you check out a file in that format it can be converted into a jupyter notebook on your side easily as well.
