I am completely with you. I know what you mean. I have the very same problems.
From the history of Markdown, why it was invented? It is dead simple. John Gruber said: "I am en editor and HTML is to clunky for me, so I will reinvent the wheel and make it easier." It is basically the very same reason why we have HTML these days, because Tim said "SGML is to clunky for me, so I will reinvent the wheel and make it easier."
You need to remember, that John Gruber is a journalist/editor he writes articles for magazines (and now for the web). Presumably, he learned as a journalist to write simple plain texts with only a few marks to indicate headlines, comments, and alike. Then the layouter would do the job and layout the text for the magazine. It is even so today how most journalists work.
Also, I have been in the industry now for some time and I see that pattern over and over again. There is some kind of standard that evolved over time, because of feature requests in-cooperated into the standard. Then there comes some guy/girl with a very simple use case and thinks "This standard is way to complicated for my simple use case. I can do that better." Then this new way gets some attention and other people are speaking out loud "Yeah, we have the same trouble for some time. Lets make that new way standard and improve from that on, now." This new way will now become a standard. Lots of people having new feature request, because this old standard can do this cool feature the new standard can't, so lets in-cooperate that into the new standard. And so on, and so on. And the wheel will start over again with a new person.
BTW, you can apply the same pattern to programming languages. Remember why and how PHP started? Because Perl was a go to at the time, but it was to complicated for some people. Then came Ruby on Rails.