The problem is that your goals and skills don't match the purpose and capabilities of the tool, not that the tool is insufficiently "intuitive".
Manuscript composition used to be: write your document by hand or with a typewriter, handwrite some notes in the margin, throw in some pages with your figures on them, then let a professional typesetter take care of all of the technical details of making a typeset document for printed output. This was a whole separate career, and the typesetter would sink almost as much time into making your document look pretty as you put into writing it.
If you are using LaTeX, you are taking on the role of the professional typesetter yourself, and you need to make some specific technical choices to get some output from it. This can be a problem if you are inexperienced and don't know which choices to make or in a hurry and don't want to make any choices, but is also good insofar as it lets you actually produce a professional quality document if you have the time and expertise to do so. The difficulty involved is at least an order of magnitude less than doing composition of metal type.
If you are using markdown (or whatever), you are just punting on having a professional document at the end, and/or letting a system make all of the choices for you (often badly), or perhaps expecting to still hand off your document to a professional at the end for proper typesetting.
