It sounds like we're treading pretty similar territory.
After about a year of using half-baked workflows I had cobbled together from orgmode, todotxt, iTodo, and various other packages, I decided to switch to Plain Tasks a few weeks ago. Almost immediately I started re-writing it to make it more Markdown-like. After a few days I gave up and went back to my half-baked system, which currently consists of the following:
A syntax almost identical to todo.txt, along with some useful commands to add and complete actions. This is where I find use for the All Fold command, because the syntax is just one item per line. I've taken the plunge and am trying to implement a full GTD system, and, although I dislike this format, I found I have the least resistance to using it.
A syntax which is a sort of fast-and-loose Markdown. For example, you can cram things next to each other without empty lines (which is not valid in strict Markdown):
# Heading 1
## Heading 2
- List item
## Heading 2
This syntax is in flux always and mostly broken at the moment.
I've gone ahead and installed the Clickable URLs plugin and chucked my own orgmode-derived abominations.
I have some mostly working code for opening local files with Wiki style links
[other-file.md]. (From the Wiki plugin).
I use SmartMarkdown but it doesn't "feel" right, although it's probably an improvement over what Sublime provides by default. Navigating a file with lots of folded coded is very annoying and very easy to erase entire chunks. I wish there was a plugin that made folded text indestructible.
I think that "zoom" is an interesting idea. It should be possible to write a plugin that does this by folding the text above and below the current location. I think a sane way of doing this is to re-write the Markdown (or whatever) syntax so that there's a scope defined between headings (including the heading itelf), otherwise you have to resort to regexs at the plugin level. (Does this make sense?)
I'm very fond of the orgmode checkboxes:
- ] Incomplete item
- [X] Completed item
For about the first half of 2012, all my organization was basically Markdown + orgmode-style checkboxes.
(Then this happened: viewtopic.php?f=3&t=7388&hilit=+usb#p34327)
I just watched the Folding Text video again, and I noticed that the ".todo" lists use checkboxes. I've been trying to figure out how to use checkboxes or checkbox-like things with the minimum of conversion difficulties (via Pandoc and the like) and have encountered the difficulty you also point out. I think I'll go back to combining the Markdown syntax with the checkboxes (and maybe some bits of the GTD syntax/commands) and worry about how to convert to other formats later.
Although I like the Workflow/PaperTasks/FoldingText simplicity, one of the things I've found really useful is to date everything, so I can refer to it later. I only need the date, not the time, but it's pretty intrusive:
- incomplete item @added(2012-02-06)
+ complete item @added(2012-05-24) @done(2012-06-02)
In my todo.txt syntax, I color it using the comment scope so that I can tune it out, but I can only do so because the dates are always at the beginning of the line.
Maybe folding these meta-tags, coupled with the orgmode checkboxes is the way to go:
- ] incomplete item ...]
- [X] complete item ...]
I'm not quite sure how this would work, though.
(Sorry for the long, chaotic post.)