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Excellent post. I agree entirely.
There absolutely must be an elegant solution to the problem. However, in my opinion, the issue is that not enough people are interested in having the security you mention. Don’t the statistics say that over 50% of people don’t use a password manager, reuse passwords and those passwords are things like password123?
This apathy towards security presumably means that there is very little money in designing the elegant solution to the problems raised in your post and many of the brightest and best in the field will simply seek alternative employment in the online data collection and advertising field where all the money is.
As it stands, so many people have so little concern about online security or privacy that it seems to be slowing progress in both fields.
What I meant by my threat model not being the tightest was that if I want to read something on a site that requires javascript and cookies then I will just turn them back on temporarily rather than not read what I want just because of possible tracking.
I agree with your point about the web being almost unusable in parts without JavaScript. However, I find that a lot of sites have a lot of javascript-heavy pages at the front but simpler pages behind where you get to things you actually want to look at. Usually a site’s RSS feeds let you get directly to the simpler pages without using JavaScript.