If the verbosity of writing \begin{description} ... \item[basis]... \end{description} is the issue, you can get around that with a couple of shorthand macros.
I also replaced all maths symbols with their Unicode equivalent. The result was very readable markdown source text, easily compiled to Latex and PDF, using a mk file.
My thesis also included formalised proofs in a proof assistant, and they were just written straight into the markdown files as code blocks, and were using the same Unicode symbols as the rest.
Later, when publishing the different parts of my thesis, this separation from Latex made it easier to convert to whatever cls the publisher wanted, since I would just change the template.
Regarding having unicode for the maths, how did you deal with symbols that needed scaling (brackets, integrals, etc.?) They may look simpler when seen as text, but they certainly won't render nicely as math...
∑_{0≤n≤k}n²
expands to
\sum_{0\le n\le k} n^2.
Some of these are suboptimal. But you can just change them, and make your own.
A Markdown -> LaTeX -> pdf pipeline was how I wrote all of my algorithm assignments in college. I wrote things like: