@zjedi I think most of what you are looking for is already possible since Hugo v0.14 (see Issue 147). Any files in the content folder that are not picked up by Hugo for processing are just copied over in the same file structure.
I have been using this a lot with images inside the same folder as the markdown file. If you don’t want to put the assets in a subfolder you will need to name your content index.md or use slug = "/" in your front matter.
You can see how I’m using it in the discussion about Content Organization Best Practice (See Structure B).
The way I reference a file in my markdown files is just with [My Image](my-image.png). Of course, if you let Hugo rewrite the url of your markdown file (for example based on the date 2017/05/20), then that will not work (maybe this issue about asset bundling might fix this - if it is actually something we want…).
What is not easily possible yet is nested sections if this is what you would like to do. There is an issue for nested sections.
Does this answer your question or am I missing something?