By far my biggest pain point is Microsoft Word. I've found that there are existing solutions for most steps in the research process (Git for version control, Rmarkdown/Quarto/Jupyter/Orgmode for integrating the code and the analyses, Zotero for citations, etc), but almost every research project that I've been a part of has eventually required the manuscript to end up in Word due to either journal requirements or some collaborators refusing to use other tools. At that point all the advantages of the other tools go out the window. It's easy for people to change tables or otherwise break the linkage between the manuscript and the analysis code, and you're stuck spending a ton of time auditing the paper and fiddling with the appearance of tables. Furthermore, once you're in Word you have to manually move any changes in the analysis into the manuscript rather than being able to rerun the code and run the output through Pandoc. I would love a tool that lets me work with collaborators in Word (including track changes) without losing the advantages of my preferred workflow.