When comparing Federated Wiki vs Org-mode, the Slant community recommends Org-mode for most people. In the question“What is the best cross-platform note-taking app?” Org-mode is ranked 1st while Federated Wiki is ranked 60th. The most important reason people chose Org-mode is:
Org-mode is characterized by a flexible and versatile system with adaptability to different workflows, making it comparable as an Evernote alternative. It is at once simple and complex., which helps it to compete as an Evernote alternative.
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Pros

Pro Stories
Arrange your personal view of a wikis content by opening local and remote pages next to each other. Shift-clicking a link will open it next to already open ones. The story will then be visible in the URL.

Pro Free and Open Source Software

Pro Versioning
Your page is the Journal of the page.

Pro Drag and drop refactoring
Recompose your contents all the time.

Pro Federation
Write locally, fork to your public site. Fork from others.
Pro Very flexible
Org-mode is characterized by a flexible and versatile system with adaptability to different workflows, making it comparable as an Evernote alternative. It is at once simple and complex., which helps it to compete as an Evernote alternative.
Pro Built-in agenda
Org-mode has some built-in agenda functionality. You can schedule tasks and assign various degrees of importance to each of them. Org-mode agenda can also be synced with Google Calendar.
Pro Versioning can be tracked and synced using Git or other VCS
Org files are plain text, and lend themselves well to version control. Emacs also has good integrations for various VCS.
Pro Great sync support
Notes and to-dos can be synced with Trello, Toodledo, Simplenote, Orgmobile, or with tools like Git on Github, Dropbox, Google Drive, and Bitbucket, while WebDAV (with iOS and Android) can also be exported to PDF, mind map, LaTeX, HTML, Docbook, or txt.
Pro Basic spreadsheet functionality
Org-mode has some basic spreadsheet functionality. Other than auto-formatting ASCII tables (a notoriously annoying problem), it also has support for LISP-like syntax to define equations or any other functionality that can be achieved through spreadsheets.
Pro Out-of-the-box Latex support
Org-mode has out-of-the-box support for Latex: it can immediately parse equations (or other Latex markup) and can even compile notes to PDF or HTML.
Cons
Con No drag'n'drop file upload
Con Difficult to learn
Org-mode has a difficult learning curve since you have to learn all the keybindings and commands. It's especially difficult if you are not used to Emacs.
