When comparing Org-mode vs Markdown, the Slant community recommends Org-mode for most people. In the question“What are the best markup languages?” Org-mode is ranked 1st while Markdown is ranked 2nd. 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 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.
Pro Human-readable
Designed to be easy for a human to enter with a simple text editor, and easy to read in its raw form.
Pro Widely used
Markdown is quickly becoming the writing standard for academics, scientists, writers, and many more. Websites like GitHub and reddit use Markdown to style their comments.
Pro De facto standard
Markdown is ubiquitous. It's supported by nearly everything. The markup available in the common subset of all the many dialects isn't that rich, but it's usually enough to get the job done.
Pro Multi-directional
You can convert HTML to Markdown or Markdown to HTML. You can use tools like pandoc to convert to other formats as well.
Pro Revision friendly
It is easy to track changes for markdown documents as compared to other formats like doc, html, etc. You only need to place your markdown documents under some version control system.
Cons
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.
Con Lacks a coherent standard
Lacks a coherent standard, just many semi-compatible dialects (MultiMarkdown, etc). This inconsistency can cause problems if the person writing the Markdown is using a different dialect from the one that will be used to render it.
Con Bad support for table
It has poor support for table, while table is an important part of article.
Con Bad support for larger documents
Works good for single file documents like READMEs.
Lack support for cross-references, TOCs, document index etc.
Con It doesn't support semantic markup
It's unstructured.