The use case for 99% of pdfs is email transfer. They are absolutely superior to sending a clunky, bloated MS Word or CAD document. The web archive is just the final resting place in the process that made them.
Same with electronic part datasheets. I need to be able to mark up and save datasheets along with the other documents which make up the design of a product.
I have been maintaining a PDF library this way using GoodReader for about 10 years now. You can connect it to most cloud storage services or any SFTP or WebDAV server, and sync annotations with Acrobat, Preview, Okular, etc. on the desktop. I have still yet to find something this good for HTML or EPUB documents.
With academic articles, I virtually never want to simply read them online.
I need to save them for future reference, read them later when I've set aside time, annotate them, refer back to my annotations four months later...
Arxiv (or JSTOR or wherever else) is just where you get the papers. It's not where most academics are going to be consuming them.
(For consumption, a full-size tablet like an iPad, with a stylus or Apple Pencil, is absolutely ideal.)