Here’s some plugins you can use to enable Etherpad to be useful for academic writing. All founds on the Etherpad plugin page with minimal effort.
Rights Mgmt: Etherpad Admin Pads
Privacy: Take your pick from the plugin page.
Footnotes: Use ep_foot_note plugin
Tables: Use the Etherpad Tables plugin
Images: Use the Etherpad images plugin
Formulas: Use the Etherpad Mathjax plugin
Comments: Use the Etherpad Comments plugin
References: Use the Etherpad Reference plugin
Import/Export: Extend import/export support with various options from The plugin page
Offline Support: Use the Offline Edit plugin
Usability: Extend usability with various options from the plugin page