When comparing Evince vs mupdf, the Slant community recommends Evince for most people. In the question“What are the best PDF viewers for Linux?” Evince is ranked 4th while mupdf is ranked 8th.
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 Annotation capability
With mupdf-gl, you can do most of the annotations and comments.
Pro Super fast
It was written in C and opengl, so your hardware was used fully.
Pro Vim-mode shortcut keys
Super easy to use with rapid response.
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).