As of late I’ve been using restructuredtext and rst2latex.py and have been quite happy with it. I’m quite used to LaTeX for writing equations and RST handles most of the other boilerplate. If you do need to do fancy TeX things you can still just drop that inline and it generally works pretty good.
Interesting! I picked it up because of Sphinx primarily. The ability to extend it to pretty easily and cleanly add things like project management blocks is awesome. The Emacs ReST mode generally works pretty good. The only thing that kind of tripped me up was the indentation rules around bullet points.
Just had a quick look at AsciiDoc and it does have some features that look really nice (e.g. the include:: blocks are quite reminiscent of how I structured my LaTeX MSc thesis). And it looks like it similarly has an extension API that would likely fit some of the project management stuff I put together. Neat!
I wrote many physical books in rst. (see rst2nitrile).
Last year I decided to join the 21st century and migrated my tool to be Pandoc and markdown based. I'm still writing code for my toolchain, but now I'm using tools that much more folks are using.