Why not rely exclusively on Org?
I think Org is one of Emacs’ killer apps. I also believe it is not the right tool for every job. When I write notes, I want to focus on writing. Nothing more. I thus have no need for stuff like org-babel, scheduling to-do items, clocking time, and so on. The more “mental dependencies” you add to your workflow, the heavier the burden you carry and the less focused you are on the task at hand: there is always that temptation to tweak the markup, tinker with some syntactic construct, obsess about what ought to be irrelevant to writing as such.
In technical terms, I also am not fond of Org’s code base (I understand why it is the way it is—just commenting on the fact). Ever tried to read it? You will routinely find functions that are tens-to-hundreds of lines long and have all sorts of special casing. As I am not a programmer and only learnt to write Elisp through trial and error, I have no confidence in my ability to make Org do what I want at that level, hence ‘denote’ instead of ‘org-denote’ or something.
Perhaps the master programmer is one who can deal with complexity and keep adding to it. I am of the opposite view, as language—code included—is at its communicative best when it is clear and accessible.
Make no mistake: I use Org for the agenda and also to write technical documentation that needs to be exported to various formats, including this very manual.