Hard to browse, bookmark, annotate (either in place or separately), cross-reference, cut and paste (as with scissors). Doesn’t help that most books are not available in a carefully crafted digital-native format.
The people I know with the most effective research habits, even ones who get most of their material online, still make great use of note cards, white boards, marked-up printouts, and the like.
For now paper is definitely preferable for reading anything but pulp novels, newspapers, and ongoing discussions. But I can imagine that changing if some people put in work on the software side in the next couple decades. Biggest pain point at the moment is probably authoring tools.
If every basic textbook was filled with interactive (programmable?) diagrams, computer simulations, extra related media, links between text and video lectures, a wider variety of practice problems at varying difficulty with full listings of hints and solutions, in depth technical annotations and bibliographic links to primary sources (viewable in place) for every chapter, etc., learning from textbooks could be made much more reader-centered, with books becoming less a serial prose format and more like a tree/graph. But all that stuff takes massive amounts of work, and would require some kind of collective funding by a group laser-focused on the real-world effectiveness and quality of the output, rather than political bullshit or rent-seeking, as most current curriculum designers and textbook publishers are. Teams of volunteers like Wikipedia aren’t really able (at least that I’ve seen) to make a novice-friendly but still accurate explanation or a coherent narrative for a whole large subject.
Your other points I think are important, but really more related to teaching materials and textbooks than journal articles. Projects like nanohub are doing interesting work in this area imo.
This is exactly the kind if situation where digital hi-res screens and zoomable vector diagrams as presentation formats are immensely superior to paper print. You're a collector and hence holding on to print editions because of nostalgia. We're however hobbled from evolving high quality modern documentation by being tired to "printability" like pdfs and Tex