IIUC, what org-mode provides you is:
1. a (markdown-like) lightweight document markup language, with lots of syntax hooks ("#+") for different tools.
2. some (even lighter, i.e., no "#+" required) organization-based syntax hooks. These are the TODO/DONE/... labels (plus the "[ ]" tidbits), the table syntax, the metadata (e.g. AUTHOR). In fact, the idea of adding metadata to a lightweight markup language is very interesting.
3. some "programmy" syntax items, including things like tags, spreadsheet-like tables, properties, etc.
4. the agenda view. This is a horizontal search on multiple .org files to create a work agenda.
5. some emacs functionality related to automatic recognition and operation on some of the syntax items. For example, org-table-align will "Re-align the table and don't move to another field".
There are lots of other features, but nothing that other lightweight markup languages don't/can't have too.
My main concerns are:
1. it is inextricably tied to emacs. AFAICT, only (5) in the previous list is emacs-only. All the other functionalities are related to the markup syntax.
2. I wish the org-mode language was fully markdown compatible (I can barely remember the syntax of one, and now I need to use 2).