What note app would you recommend?

Both the rich text editor and the mobile app are in need of a bit of TLC in a number of places:
See below for editor related topics as a possible GSoC project:

Or this list of mobile improvements in general

However as for:

and

I agree that Markdown is a choice amongst other formats but I would argue it is also one of the strongest as it is widely supported, widely known (even Reddit uses it for its comments) and allows a lot of seamless features without the need for some kind of extra conversion library. Even if Joplin itself blew up you could still just grab the notes directly from the database and have all your data intact, just how you wrote it.
Not to mention the number of markdown related tools available as node packages which can be used by the plugin system.