When comparing Evince vs (Spac)emacs with pdf-tools, the Slant community recommends Evince for most people. In the question“What are the best PDF viewers for Linux?” Evince is ranked 4th while (Spac)emacs with pdf-tools is ranked 12th.
Ranked in these QuestionsQuestion Ranking
Pro Free and open source software
Pro Can annotate a pdf
It isn't immediately obvious how to do this, but the instructions are here.
As of 13 June 2018, the icons/screenshots on that page look different than what can be seen under Evince v3.18.2, but the devs have been alerted to this discrepancy, and there are requests they make the finding/using of annotations more intuitive than they are now.
Pro Can find a word in a pdf
Pro Supports touchpad gestures
Pro Good integration with Gnome desktop
Pro Supports touch interaction
Supports touch, including drag and pinch to zoom.
Pro Can play embedded video
To my knowlegde, the only PDF reader on Linux that can play embeded video (unfortunately not in presentation mode, which is a major drawdack).
Pro Search results list
Click/tap the magnifying class in the top bar.
Pro Synctex support
Pro Easy installation
Although installing requires little more work than stand-alone readers, pdf-tools is very easily installed via Emacs 'list-packages' or even easier as a layer in Spacemacs
Pro Convenient default keyboard shortcuts
Uses emacs or vim-style navigation (via spacemacs/evil. Shortcut overview via transient state "SPC m .")
Pro Automatically exported notes
Notes can be exported automatically to and backlinked from an external org notes file using the org-noter or interleave package
Con Scrolling is not smooth
Con Window can't be resized
You can only read in a small box or fullscreen, no way to manually size window.
Con Tied to GNOME
Comes with all those weird things like popovers and clientside windows.
Con Keyboard shortcuts cannot be rebound
Con Thumbs not working
Scroll once, and all thumbs in the side panel are gone.
Con Poor UI
Since version 3 it is almost unusable.
Con Unicode Problems
Some languages other than English do not render correctly
Con Adding annotations isn't as intuitive as it should be
Instructions can be found here. Specifically, a user should be able to select a word or block of text, then right-click and see highlight/add note options in the drop-down menu. Currently, this option isn't available (as of Evince v3.18.2 / 13th June 2018).
Con Only for power users
Handy only for people that want good notes/annotation management. Otherwise using any other pdf-reader is recommended
Con Requires emacs
Con Too cumbersome for quick reading or annotating
Although setting up pdf-tools is not too much work. For quick reading using some default pdf-viewer like evince/okular/zathura is recommended. Also, except for the auto-export feature (with org-noter/interleave package), other editors like e.g. pdf-XChange Editor (via wine), Okular or mupdf have even more powerful annotation features.