PS: Why not have the best of both worlds, that is, Markdown and Wikitext? Yes, you can; see Texti (Text with Formatting Instructions) - https://texti.github.io
Having hash line comments is probably a non-starter in a text format (the latex % syntax is probably a better idea indeed if you want line comments). Also the -- strikethrough -- syntax will probably conflict too much. You want comments to use a syntax which is otherwise nearly unused.
PS: The main missing feature (among others) in Markdown and that rocks Wikitext (and Texti too) is built-in (recursive) templates (with optional parameters) using the {{}} syntax.
[1]: I know % is not new because it's used in LaTeX but LaTeX is esoteric compared to Python, Ruby, Shell Scripts, Unix Configs, etc.
#1: That's the only reason.
It's kind of like:
1. FC Köln - that's a football club name (and not a list marker). Try it in markdown - same gotcha :-)