I agree; you're right. It isn't easy. I wouldn't want to go back and figure out my TikZ/PGF diagrams if that package lost backwards compatibility. But at least there is hope that a straightforward LaTeX document can be read in the future. You can always run the LaTeX source through Pandoc or just read it as it stands as text with markup. It's better than having a WordPerfect or XYWrite document (I liked both of those better than Word way back when).
Your idea of a VM container is interesting--I hadn't thought of that, but what about the software to run the VM. Does VirtualBox stay backward compatible over the next 10 or 20 years? Maybe the way to go is Markdown, that is so easy to read even without processing it.
I don't expect it to be 20 years backwards compatible, but since I use VMs daily, I have a good idea of when to start looking for a way to convert the machine to a different more modern format.
Re: markdown or similar like restructuredtext, I don't have any experience with advanced markup in them, but I think you'll have the same plugin problem as with LaTeX. The readability of the source isn't that important, since you'll probably have the rendered output as well, and that is,or should be, copy/pastable if needed.
Your idea of a VM container is interesting--I hadn't thought of that, but what about the software to run the VM. Does VirtualBox stay backward compatible over the next 10 or 20 years? Maybe the way to go is Markdown, that is so easy to read even without processing it.