But there have been a few genuine innovations. Personally, my favorite is the notebook - whether from Rstudio, Mathematica, Jupyer, etc. especially when you add dynamic widgets like D3 or maplets.
It allows not just literate programming, but quick prototyping and verification, by integrating visualizations. Sometimes you can even embed your datasets for replication.
I would love to see scientific publication move to notebook only - as it, I want to download the whole thing and do some tweaks to see if I can poke any obvious hole, or if it is genuinely interesting.
When I say the whole thing", I mean it. I do not want just the authors verbiage and some screenshots of their tables and graphs. I want their data, their formulas, their visualization, already implemented and ready for tweaking without imposing any extra software dependency upon me.