Thank you, this is very extensive and informative.
I think the second best option is to put this on its own website, something like ealibrary.org or such. Then we would have complete freedom in modifying all parts (design, structure, meta data and similar for search engines, social link integration, etc. etc.) and it's more focused, easier to remember/point to/etc.
I did something similar with http://whatistranshumanism.org/ that is entirely based on the existing transhumanist FAQ that I felt was pure gold content-wise, but hidden deep within the H+ website, poorly laid out, not working at all on mobile, and many other things. This website is now the third result on Google when searching "what is transhumanism".
The website is hosted on GitHub meaning anyone with an account can suggest edits through pull requests, or make them directly if they have write access. Although decentralization can be a useful principle, I've found that having some sort of smaller group of editors makes vetting, structuring, and publishing a smoother process and yields a higher quality end result. Anyone is still free and encouraged to provide materials, of course.
Considering your point of view regarding difficulty-then-topic versus topic-then-difficulty, I think you are right and that your suggested structure is the better one. Topic is probably a more natural way of digging in for visitors of any level. As long as difficulty is clearly communicated (words, color coding, etc.) it will be fairly easy to navigate in the sense at the same time.
Maybe we could make an inventory of existing reading lists that could possibly be considered succeeded by this new one, and once up and running that the maintainers of these can be contacted about the possibility of being merged/redirected to the new website. (Obviously some existing ones should not follow this path and will instead be linked to from this website.) In other words, an inventory of potential "mergers" versus "co-existers".
These are some of my thoughts on your questions, looking forward to others' views.
I have been thinking about this. One risk is that of increasing resource proliferation, i.e. that by adding more web pages for some purpose existing ones already fulfill, it will actually make it harder for someone to find either, or deem any of them more "authoritative" than others.
So one vast improvement to this project on top of the already excellent work you have done to extend the reading list/library and that everyone involved have done by providing the reading in the first place, would be to think about where it should live and how it is presented.
Judging by what happens when you google "effective altruism" the obvious place to keep a "semi-official" reading list/library is somewhere at http://www.effectivealtruism.org/
Specifically, I would suggest that clicking "Learn more" on the start page, then "Read more about EA" at the bottom of the page, should end up on another page on the same website with this entire reading list, divided into the three suggested levels (beginner etc.) so that it is obvious where to jump in. (The read more button currently points at http://effective-altruism.com/ea/6x/introduction_to_effective_altruism/ which is a somewhat sparse and partly outdated list of reading.)
Which brings up another important aspect that could help this project a lot: to make sure outdated resources (or those that have been superseded by better ones for the same purposes) disappear from the web altogether, or even redirects to the new page once it exists. This obviously needs to happen through friendly discussion with those behind all the other pages. To make sure people end up at some pages rather than others, combined with other search engine optimization techniques, is what could really make a difference when it comes to steering people in the right direction.
However great the reading list (and let me add again that it is really great!) it won't matter if people don't find it, and the best way to make that happen is to put it in the most obvious and easiest to find place.
Sorry for the braindumpy quality of this reply, please let me know if anything is unclear and I'll try to clarify it. What are your general thoughts on the above?
P.S. By profession I'm a web developer and I'd love to help out with the more technical parts of this project, if that kind of help is needed.