>should be the reader's choice, not the writer's
Sometimes. There are a lot more design options available if the creator of the content maintains control over layout, fonts, etc. Sometimes this doesn't matter--if it's a block of text for example. Fairly simple layouts also render pretty well on the web.
Different content works better or worse with different approaches. One isn't intrinsically superior.
On the other hand, how does one write a standard invoice or a tax form using only plain-text / markdown? Formats with control over the layout have their place.
In addition PDF adapts, by design, a model of paper to the web. It's a "horseless carriage" file format.
Font size, page width, cut/paste and presentation in general should be the reader's choice, not the writer's. The Web manages this, sort of.
The OP is right on in this regard. Even the TeXs of this world, while better than the binary formats, have upgrade complexity.