Really glad to hear you guys are aware of this! I do love the expressiveness and ease of understanding that interactive diagrams offer, but find the prospect of a mutable scientific literature to be a somewhat horrifying one. I understand and completely agree that academic authors can not reasonably be required to become experts in web design.

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From my perspective, the main issue seems to be broken formatting and media (alignment, hoverable citations and notes, missing or partial images, etc). The recent activation atlases paper is a particularly good example of the problem (https://distill.pub/2019/activation-atlas). I don't have time to tally up all of the differences right now, but briefly just a few big ones so we have something concrete to refer to here:

* The index.archive.html version shows "Loading..." in place of all the images in the first figure (and most of the other figures as well).

* The Zotero web page snapshot version actually does have the images for the first figure, but that figure still has other issues. Many of the other figures still just show the "Loading..." text though.

* In both cases, text is flowing around the figures in strange and unreadable ways.

* The bibliography for the index.archive.html version is completely broken.

* In both archive cases, uMatrix is showing third party scripts running on the page. I've allowed them, but obviously loading things from remote locations means it isn't really standalone anymore.

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> we haven't been able to think of a satisfying automatic way of providing static fallbacks to interactive diagrams.

Why does it have to be static? Why worry about graceful degradation at all? I guess I just find myself wondering why there would be two versions of a scientific paper (ie "real" and "archive") in the first place? I don't see any reason why scientific work needs to be published in a static medium, but it does seem like it should always be standalone and immutable.

To that end, why not require submissions themselves to be fully standalone entities with absolutely no external dependencies (ie review them without internet access) and then just publish those? Then instead of pdf papers, you end up with interactive (but standalone) html papers that are viewable in any standards compliant web browser, scripts and all.

Barring such a drastic solution, I don't have any clever ideas from a technical standpoint; I'm not a web design expert nor am I familiar with what tooling you allow authors to make use of in their papers. A fairly blunt approach might just be to require authors to provide static images as standins for each figure. It could literally just be a static image of what the interactive figure initially looks like before you do anything with it. Then you'd just have the existing formatting issues to sort out, but presumably those are fairly straightforward.

An aside: Figures don't seem to be numbered in the activation atlases paper I referenced above. It might be nice to add a requirement to clearly number and label figures, tables, and other such insets - as far as I know, all the major academic publications do this. If you're wondering why, at minimum it makes it much easier to discuss the paper when you have a clear label such as "fig 3a" or "fig 4 panel 2" or whatever to refer to.