HTML is not for writing but for creating UIs. That was why it was created anyway. Markdown was specifically created for writing. It has no other purpose.

Saying that Markdown is bad is really naive. There are not many ways to specify formatting without it getting in the way of your writing. Markdown is popular because it strikes the right balance where reading a markdown document requires a lot less visual strain compared to the same HTML document. It requires the least amount of letters to specify formatting - italics is 2 chars, bold is 4 chars, underline is 2 chars etc. Lists are mostly inferred and require no additional formatting. Compare that to HTML which requires 5+n chars (where n is the number of chars in the tag name) regardless of which format you want to use.

Markdown does have it's quirks but they don't come up 99% of the time unless finding them is specifically your intention. Knowing whether *__hello__* is bold italic or italic bold is not important unless you are writing a parser.

The downsides of Markdown are much, much less than the downsides of HTML. Writing is not the same as designing a website or a UI. It's not meant to be pretty and typesetting + styling should not be the concern of writers.