When comparing Master PDF Editor vs (Spac)emacs with pdf-tools, the Slant community recommends Master PDF Editor for most people. In the question“What are the best PDF viewers for UNIX-like systems?” Master PDF Editor is ranked 11th while (Spac)emacs with pdf-tools is ranked 15th.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Built-in OCR
Pro Free for non-commercial use
Pro Very good import capabilities
Pro Only cross-platform editor that can handle LiveCycle Dynamic XFA forms
PDF-Exchange can handle XFA, but it's Windows only. XFA is usually created in Adobe Acrobat.
Pro Extensible, customizable and scriptable
Being a Emacs plugin you can use elisp to customize, script and extend pdf-tools.
Pro Can treat multiple PDF's as one big PDF
Pro Nice search using Occur
Occur creates a list all lines matching a regexp or string in one or more pdfs and allows easy jumping between them. Really helpful when searching long documents like datasheets.
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.
Cons
Con Proprietary, but reasonably priced
Con Free only for non-commercial use
Con Only for power users
Handy only for people that want good notes/annotation management. Otherwise using any other pdf-reader is recommended.
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.