Org markup should replace Markdown
It does everything Markdown can and much more. And it's older.
Emacs isn't everyone's cup of tea, but it was a mistake by Github to latch onto Markdown. Now we are stuck with such a limited markup format with so many incompatible versions--none of which are as adept as Org syntax.
I'm guessing it's because Org markup was not embraced early enough by non-Emacs users that Github didn't do it. I like markdown, the limitation is exactly what makes it great. It's just the essentials for flowing text, not another scripting layer, html preprocessor or anything like that. Also the syntax of markdown is nearly as reading the resulting rendering. Everything you said is actually true of Org. It is a markup language that looks like plain text but is far more capable.