That is leagues ahead of native PDF plugins which are slow, buggy, full of vulnerabilities, closed source, require a deprecated plugin infrastructure and usually can't edit documents either.
PDF.js is one of the better things to come out of Mozilla.
Sure if it piques my interest I would download it, organize it but I wouldn't go through the pains of doing that for every pdf I lay my eyes upon.
You don't have to do that. Just set your browser to open the file in a real application. It'll automagically download to some temp dir (ie, /tmp) and you won't have to care about file paths or organization at all (unless you want to).
I have tens of research papers open in my tabs at all times. But for a good experience reading I open the full text in my pdf reader.
We can dislike it, but we need to reconcile it.