Mozilla has developed a PDF reader addon for Firefox using javascript. I've been running it for about a week as my default PDF reader. It's been acceptable for my needs.
Interestingly they are working on a JS version of flash called Shumway[1], so maybe, just maybe future FF (or even Chrome if it works there) will be able to translate Flash to JS, for your iPads and whatnot.
It is built in in stable (at least it seems to be in the stable version in the Arch repos), you just have to enable it in about:config. If I remember correctly 'browser.preferences.inContent' has to be set to true and 'pdfjs.disabled' has to be set to false.
I believe it becomes built-in in Aurora and Nightly builds.