Every developer needs to learn two lessons about great interfaces:

1. Layout, format [aka style], and interactivity, is both hard and necessary

2. Interfaces are subtly complex

Number 2 is the reason that "simple" formatting markup, like Markdown, will never be good enough to make a great interface. You can make a poor interface with Markdown, and that poor interface is good enough for very simple use cases. But people quickly get annoyed by simple use cases. They create friction, both for the designer and the user. More useful functionality is desired, and you need something more complex to enable that.

I've written a lot of tech docs. Markdown is one of the worst methods I've found to write them. Not because its formatting isn't intuitive, easy to remember, and easy to use. But because the documents it creates are not conducive to the purpose of the document: making it easy to read and remember information.

As for more general interfaces, the easiest way to understand why you need more elaborate methods, is HTML. When HTML was created by Tim-Berners Lee ~1990, he intended for format and layout to be independent and configurable. However, for years it lacked both formatting and layout options, and lots of people complained. It took six years for CSS to eventually become a standard, and before that, lots of hacks and incompatibility (and it turned out, more of them afterwards). The entire time people were complaining about how any document editor could easily format and layout exactly what the author wanted, but web browsers persisted in being difficult and inferior. Tables were only added in HTML 2.0, five years after the Web's birth.

You can still get by with not-very-good markdown, for not-very-good interfaces. But you will never have a Great interface without the ability to control layout, format, and interactivity, in subtly complex ways.

There is no easy way for a human to do that with text. But there is an invention that enabled users to create complex and rich layout, formatting, and interactivity: the WYSIWYG interface. With this tool, the human no longer needs to remember control characters, markup syntax, or formatting codes. The user no longer needs to spend endless time typing in code, displaying the result, being unsatisfied, and tweaking the code again, trying desperately to just get the screen to show them what they know they want. A WYSIWYG editor enables a human to completely discard any knowledge of how to format or layout content, and instead simply move things around on their screen with a mouse, completely eliminating complexity for the human, and enabling the creation of better content.

I think the reason modern software abandoned WYSIWYG, is that modern software isn't created for users. Most modern software is open-source (or close), and as such, it's created by developers, for developers. Developers don't want to spend time engineering a WYSIWYG, because they have no need for a good interface, and they don't care about wasting their time writing code. To them, writing code is the whole point, regardless of how long it takes, or what the outcome is. That's why Markdown was invented, and why people persist in trying to force Markdown to make something better, without realizing that that's impossible. They want to to build a castle, but they don't want to use anything other than the twigs and rocks lying about their feet.