But is there really a good reason to not just keep these in browser? I don't really know if there's much value in reading these locally. Maybe this would be a good fit for an electron app?
* A way to save back form data. I believe google is working on a js api to access local files (given a few conditions). * A way to bundle the html with every js script, ressource, css, etc, in one file, without making a huge mess.
If you had a tar.gz with an index.html inside, and the browser was to transparently allow r/w access to the archive contents from contained js scripts, this could solve a lot of use cases (heck, even "electron" apps could be replace by this). One exception being printed documents (postscript), at which pdf is quite good.
That behind us, there's also a matter of reliability and control. Services live much shorter than data they process; given today's trend, I wouldn't expect an online-only paper to be available after 5-10 years. Having a self-contained bundle would let me archive it independently, and would prevent any third parties from being able to interfere with my reading/exploration.