There is not a good answer. Markdown is a poor format and there are a number of almost compatible variations. However Markdown in all formats is somewhat limited and so there will be some things you cannot do that if you work on a complex project you will want to work on.

However markdown - if you stick with the subset that everyone supports is the most widely supported alternative. If you go with a specific markdown you lose support for something else you might want. If you go for non-markdown you will lose support for most of the world.

I personally selected restructured text which is really powerful for the complex documentation I'm trying to create. However I keep running into nothing else supports it problems (I can extract doxygen from C++ - but only with tools that don't support the latest. I haven't figured out what to do about Rust documentation)