I think Markdown was supposed to be less fiddly than HTML, which it probably accomplished. Some of Markdown’s features, like tables, I find easy to forget and there are different dialects of Markdown. I can agree those are drawbacks.
Advantages Markdown has - for me, and my mileage always varies - are smaller file footprint and the ability to transclude.
If I have a Markdown file that’s offers support for what I’m writing, I’ll sometimes transclude the second document. That way, if things change in the supporting document I’ll see the changes in the first.
For instance, you’re writing notes about a section of software documentation that ties some low-level principles together. Including a live version of another file can be helpful.
If the design evolves and new aspects enter the low-level principles, any edits on those notes automatically appear in the higher level notes.
Tagging, replicants, and annotation files are also solutions for that kind of thing.