Since ST3 now allows for a much easier to work with syntax file format I would like to suggest changing all the syntaxes of MarkdownEditing (MDE) to the .sublime-syntax format. Or, since you probably want backwards compatibility with ST2, providing both formats.

This would have several advantages, but most of all this would allow for derivate plugins of MDE to include required syntaxes in their own syntax. As an example: Even though I am very unexperienced I would like to develop a "plugin" that provides scope selectors and maybe coloring for the syntax of my very often used wiki generator of the name ikiwiki named ikiwikiEditing. Since I like the features of MDE and don't want to develop a Syntax all by meself, this would allow for easier integration of already done work in future derivate plugins that provide additional syntax on top of the enhanced markdown you already provide.