Would be great to be able to sync the html annotation export to Evernote automatically - shouldn't be too hard to implement. Just save the annotations made in a new note in Evernote and keep it updated when new annotations are added. The note could have the paper's reference as title.
We are planing a big overhaul of notes taking and export for 2017. Not sure if we are going to consider syncing to Evernote, but exporting a file that can then be uploaded to Evernote will most likely be included.