I think markdown and org derive from the different demands, while they coincidently have the similar markup syntax to edit plain text documents.
Markdown is only designed to easily read/write plain text. Refer to its philosophy:
Markdown is intended to be as easy-to-read and easy-to-write as is feasible.
However, org is more complicated and it also has more features. You can use org for GTD, maintaining TODO lists, project plans etc. And the markup syntax seems just one accessory in the whole org system.
In my options, if only write some plain documents, you can choose anyone as you wish. However, if GTD or intend to export your plain documents for more formats (tex/pdf/docbook), you have to choose org.