Yet Markdown languages are far, far more limited in both scope and functionality than HTML is. How do you bridge this gap without making it just as complex?
That's a really big topic but in general I'd combine theming and markup to one language (not necessarily coupling CSS and HTML in one file but having something that does both with similar syntax and rules), make things simpler so there's one clear way of doing something rather than using a generic container for everything, etc.
No matter what you propose, unless it’s 100% absolutely perfect (and nothing ever is) you’ll end up in the same situation.
Obviously deprecating a few things will happen over time but the reason web dev is how it is now is because technology used to be a lot more limited and websites were a lot simpler. 25 years ago, nobody knew what the "modern web" would look like so it was made up as people went along. We know what specifications we would need now if anybody went back and re-did them, I think you'd end up with something better.
People say the same about no-code frameworks. There’s a good reason that stuff doesn’t work beyond the absolute basics.
I don't think they're comparable. You won't use a GUI and drag-and-drop for everything obviously, you'd still be able to add sections with code.
The fact that Wordpress powers almost half the internet is proof that a simpler web dev experience like this is in demand and it can work. Most websites don't need something complex, just something that supports rapid development and is intuitive, and doesn't make it easy to fall into bad practices. Like I said, it's a hot take, but I would prefer it so much this way.