Most "web fork" ideas try to either ditch the web as a sandboxed application distribution platform or to ditch the web as a hypertext-based front-end for networked systems. IMO a good from-first-principles solution wouldn't abandon one or the other but instead split them into discrete components. I suspect this would simplify things a lot vs. the HTML/CSS/JS status quo.

We kinda sorta almost had that for a short period with Flash (and Java, I guess): a webpage either didn't use flash and was secure and efficient like opening a document, or it did use flash and was featureful and interactive like an application. Users and system administrators could block Flash or enable it conditionally while expecting most of the web to continue to work, which in hindsight was actually pretty nice from a security perspective.