I believe we will be using PDF and other “advanced document formats” in the years to come on mostly all computer and computer-esque devices (as pointed out above.)
However, that doesn’t mean one HAS to use one specific document format. There are others, such as DjVu which is, in my opinion, a lot smaller than PDF documents. This isn’t always the case but its made for scanning documents and supports layers. While many devices today need an app/plug-in to view it, as DjVu isn’t as well known as PDF, it uses layers so you get the “text” version of the page then the visual version, which is something I haven’t seen on PDFs.
Unfortunately, I believe that there’s no way around these documents. What is comes down to is just what “container” you would like to use. However, that doesn’t mean you can’t combine all the magazines in one folder and 7z them so they are small and portable.
Until the day comes that someone makes it possible for one to “load” the container as many pages that can be controlled by HTML/CSS/PHP/JS we probably won’t have a “decent” solution.