As a TinyMCE developer. I see markdown as an alternative to HTML source editing not an alternative to wysiwyg rich text editing. It's like comparing apples and oranges.

Also the three types of content editors feed to different needs and users and I guess it's up to the user to decide what method they like best. They all have pros and cons.

Source code editors like markdown or html seems to be a hit with developers and pro users. It has the ability to do exactly what you want it to do since you have 100% control. However it's a poor user experience and hard for non tech people to learn.

Rich text editors like TinyMCE gives the user the ability to format contents without knowing anything about the source. It's also a familiar way of editing complex contents that has been around for ages. However it's easy for users to produce messed up contents so it needs to be configured restrictive.

Block based editors that enables you to separate your page into content blocks that can be added/removed has the ability to be very strict with output but lack flexibility. Say you want to add a image to a table cell for some reason unless the there is a content block editor for that particular case it needs to be a rich text editor.

From time to time I see people just bashing the shit out of our product. The problem I think with any rich text editor is that it never does what you want it to do at a code level and it never will unless you configure it exactly to your needs. Also people tends to be very angry when we remove or alter HTML contents that isn't valid according to HTML specs.
And in the case of WP the wpautop feature seems to be the cause of frustration when it comes to switching back and forth between the visual editor and the source editor.
If it's bugs in our code please report them. If we don't know about them we can't fix them. Some of them are hard or even impossible to fix due to browser limitations/bugs but most can be worked around this is what we been doing for the last 10 years.

Markdown is sure nice for simple content and a.f.a.i.k. it was it's intended purpose. For example handling complex content like tables in markdown like syntax is either not possible unless you do it in HTML or very tricky as in wikitext. Also it's not a standard so the syntax for the more complex stuff seems to be a bit random when it comes to implementations similar to bbcode. Hand coded HTML is at least a standard.

Anyway. I think the best way is to let users or web site developers decide what tool they want to use. And that is what the WP guys have done so far.