References to third party websites that can break. HTML is a living spec, so browsers can decide to break things that work today (as happened with Marquee for eg).
Even if you disallow JS entirely, and stick with just HTML/CSS, it has enough warts to not look and behave consistently over time.
A link could easily be a URN that identifies the target by its hash, all the protocols for that are already in place e.g. magnet links.
PDF doesn't have JS and hyperlinking, so I guess all you'd need would be HTML, even ignoring CSS, which could be tailored to the reader, e.g. Latex style, troff style etc.
Vanilla html with images embedded as data URNs should be pretty darn portable for the forseeable future.
Heres the kicker, it's a text based protocol, and a dead simple one, eben if we should loose all browsers in the big browser war of 2033, its super easy to reverse engineer. PDF not so much.
A subset of HTML + CSS (+ ECMAScript?) could replace PDF for this purpose. However, is there a standard subset and familiar, understandable tools for working with it? In general, using the 'save as' function in a web browser won't produce a document that looks the same 10 years later. Rewriting the source document using a tool like wget can achieve this, but it doesn't always work (eg. what if the content was pulled in asynchronously?), and you need a computer expert to create and explain how the archived format relates to the live content. 'Save as PDF,' despite its technical inferiority, is easy and widely understood.
HTML/CSS is extremely backwards compatible, modern browsers don't have problems of displaying the page differently.
How does pdf solve link rot problem? Pdf is good for print, it's consistant. But fails when display size other than big screen, especially e-ink displays that don't tend to be your standard A4.
PDFs don't solve link rot. But in HTML, it's conventional to rely on links for stylesheets and sometimes even content (images, asynchronous DOM elements), so link rot is a bigger problem.
Yeah for publishing you don't want content in links, but you can solve that with data URIs that embed images and other data directly into the link [1].
Even if you disallow JS entirely, and stick with just HTML/CSS, it has enough warts to not look and behave consistently over time.