So big caveat: my experience with Emacs is pretty much entirely limited to org-mode (which is the only reason I picked up Emacs at all). I really liked a lot of the ideas in org-mode, but the more I used it the more I really wanted to make some minor tweaks. No problem, I thought. Emacs is famous for being super customizable. But everything I touched was extremely brittle, and essentially impossible to configure to work as I wanted it to.
1. Wasn't a huge fan of "\star" "\star\star" "\star\star\star" as the headlines. I would prefer "\t\star" "\t\t\star" "\t\t\t\star". Hmm, seems the only way to do this is a hack that changes the leading stars to the same color as my Emacs background. That's kind of hack-y. The rationale I could find for this was to keep a consistent on disk format. I guess that makes sense, though it's not something I care about ... I don't intend on sharing my TODO list (and my understanding is there's no 100% compatible org-mode parser outside of Emacs anyway). Not a big deal, I'll live with it.
2. Agenda view. As I started using org-mode more and more for task management I decided I needed a good task view. I set my own task and project states (nice: simple, works) then I set to work on creating a nice view of all my tasks organized in separate sections (REFILE tasks, active projects, active tasks). Hmm, now it takes multiple seconds to refresh my agenda view. And I have to manually refresh it any time I make a change to any file ... This kinda sucks. Might be a solution for this, never got around to investigating.
3. File structure for my org files. Despite the occasional org-mode article on Hacker News, it's actually pretty hard to find good examples of a full org-mode workflow. When I was actively working on this I found one or two. When writing my org files I kept running in to the odd problem with certain features because of how I was laying out my files. Should there be an empty line after a headline? Are paragraphs separated by empty lines? If you don't do this correctly (and since there's so few examples available, "correctly" is something you have to figure out by trial and error) then certain exporters (pdf, html) don't give correct output, or folding doesn't work.
4. Directory structure of my org files repo. I like being aggressive about breaking things up in to different files. And then organizing these files in to different directories. New project? New directory, new project org file. Let's make a separate file for research. So <PROJECT DIR>/Research.org. Unfortunately this butts up with how org-mode assumes you have things organized (which again, you can only really figure out by trial and error when things don't work). Take REFILE for example. It tab completes by file name. But problematically I now have a lot of files with similar names (e.g. Research.org) in different directories. org-refile-use-outline-path sort of fixes this but it's still clunky.
5. Emphasis. The straw that broke the camel's back. All of the above were minor and I kept with org-mode. It sorta worked. But I was annoyed. Eventually I started doing some research that involved quotes where I really wanted to basically highlight phrases or sentences that were important. I figured this would either be built-in to org-mode or easily added in my Emacs conf. I never did find a solution that actually worked. I can underline, italicize, bold, etc, but no highlight (i.e. classic yellow background for text). Apparently org-mode deliberately prevents the end user from adding their own custom emphasis formats in order to have a consistent file format.
At this point I left org-mode and emacs all together and ended up writing my own rich text editor so I could do whatever formatting I wanted. It doesn't do 1% of what org-mode can, but dammit I can highlight in 6 different colors.
I'm disappointed I never got to experience the Emacs nirvana that all these articles describe. Maybe it's just org-mode, but everything I touched seemed extremely brittle. Felt very much like I was forced to do it the org-mode way. It was really disappointing.