Its flat/non-recursive/non-nested nature, by which I mean that you mostly cannot write "arbitrary" markdown inside most elements, and if you can, you have to be very careful with whitespaces/indentation/etc.
The impossibility to easily interlink to arbitrary parts of the document.

To solve both issues, I'd like to propose an extension that allows "simply" using braces (or some other punctuation pair) to allow nesting, with an option to tag/add attributes to the contents like that.

In some more details:

The format would just be `{ content }` or `{ content }{#id .class}` to be able to add attributes to a block.
If the content between braces contains new lines, the first new line sets the indentation level for the rest.

There could be a point to be made to put the attributes before the content, but I'm not sure what kind of form that would take. Maybe something like `#id{content}{.class}` could be used: only the identifier can come before the content, and has to be a valid identifier (alphanum, underscore, dash)?

I think this syntax would not clash with that much of what's already existing: mostly just the already existing attribute syntax. A potential solution to that would be to use a different character pair for nested blocks, but `[]` is already used a lot.

I've looked at implementing that as a custom filter, but I think it has to be an extension baked in pandoc itself.

Cheers