I've been studying org-mode for a few months now, and I think I'm finally getting the hang of it. It's really overwhelming, and I really appreciate the efforts that must have gone into the manual and the worg project. But I think it still needs work.
The fundamental problem is that org-mode isn't a planner, it isn't an organizer. It's a toolkit full of tools which people use differently, in lots of ways, to build their own planner/organizer. To understand org-mode, you have to understand all of the tools available, and the options you have for each, and the ways they interact with the other tools. In my opinion, the documentation doesn't explore the interactions well enough, it doesn't present the tools in an order that is conducive to learning, and it never explains why you might choose one option of tool instead of another.
For example, let's take Archiving. The documentation I'm reading right now, at http://orgmode.org/manual/Archiving.html#Archiving, puts archiving in "Document Structure", section 2.6, before TODO keywords, tags, the agenda, or anything else. There's one paragraph about what archiving means, then five or six paragraphs about how a headline with the ARCHIVE tag behaves, and then a section about moving trees and where you could move them. It isn't clear what workflows you might use Archive Sibling in, or why C-u C-c C-x C-s would archive *children* of the selected headline instead of the headline itself.
Another good example is TODO keywords, categories, and tags. It isn't clear what they all are, or why they are distinct, or what the differences are, and it's easy to confuse them with similarly-named but completely distinct concepts like properties.
In other words, to really understand the manual, you have to read it twice -- once to hear about all the concepts, and once more to see how they relate. And then to start using org-mode, you have to play with a bunch of different possible arrangements of the concepts, see which things you like, and finally settle on an arrangement that suits you a little bit, before starting the endless path of tweakage.
Reading HOWTO's like Bernt Hansen's and Charles Cave's are really interesting to see how people work, but even documents like these don't explain *why* they set things up in this way. For example, Bernt Hansen's document explains that his toplevel headings are "main categories", and shows that they each have a CATEGORY property, but doesn't explain what that buys him, or what problem that solves.
In short, after studying org-mode for a long time, I finally feel ready to start using it -- not that I understand it, but that I know where the most important knobs are. I feel like it would have been a lot easier for me to start using it if I had started with a tutorial that explained a single workflow and how org-mode supported it, and I feel like the org-mode manual could have gone a long way in making this learning easier. For example, the documentation for C-u C-c C-x C-s could say something like "This supports workflows where there is a top-level Projects heading, and each heading underneath represents a project. You could then use this command to archive all projects which didn't have open TODO items.".
I wish I could offer more concrete improvements in the form of patches and so on! Maybe as I learn more about org-mode I can do this too, but I wanted to offer this criticism while it was still fresh in my mind.