I recently removed my PDF reader and use Firefox to read PDFs. For that, I created a new Firefox user account, set it up accordingly (with a few dedicated addons, plus making manual CSS changes to the user interface). Then I created a script (in Linux) to run a file or url with this user account instead, associated the script as the default application for the .pdf file format.

Script: firefox-reader

#!/bin/sh
exec firefox --profile ~/.mozilla/firefox/xxxxx.reader -- "${@}"

To create a new profile, you can run Firefox with the commandline option firefox --ProfileManager. The rest is pretty much self explanatory in my opinion.