If Evernote integrated Markdown into its mobile, web, and native editors, I would be much closer to an ideal. It's early, but Classeur shows potential to fill this gap.

I tried http://Marxi.co, the so-called "missing Markdown editor for Evernote," but had enough syncing issues during the brief ten-day trial to put me off purchasing a subscription.

There's also a Sublime plugin that offers two-way Markdown conversion into Evernote, but I only have Sublime as a native app, not on mobile or web. https://github.com/timlockridge/SublimeEvernote

Perhaps with Evernote's renewed focus on core product, they'll take a look at improving the experience of the text editor.