> The end user doesn't want Geminispace, they don't hate that web publishers get to control layout and design, or that sites can be more complex than even the early web allowed. They don't want to write their own clients or stylesheets, they don't want the web to only be strictly static documents, with "apps" quarantined elsewhere.

I do not agree. Many users do want it. The problem is that web browsers are not written for advanced users.

(Furthermore, there are other protocols for other things, such as IRC, NNTP, etc.)

> They don't want a different markup language.

The actual problem is that even if you use a different markup language, you cannot easily serve it and allow end user customizations to decide how to display it (possibly using a more efficient implementation than the HTML-based one), and you will be forced to serve HTML instead, making it more difficult to write an implementation that does support the other formats.

You could use <link rel="alternate"> to link to the source document, or you could have my idea of the "Interpreter" header, which also allows to polyfill picture/audio/video formats in addition to document formats.