This is somehwat geared toward my specific preferences as a social scientist, but my cookiecutter template contains pretty much everything you need for academic writing using pandoc: https://bitbucket.org/jboy1/cookiecutter-pandoc-paper

You can also consult Kieran Healy's guide here: http://plain-text.co (again, this targets social scientists)

Me too. Particularly I am interested in knowing if the setup auto-suggests items from the bibfile when typing [@

That's a big one for me that I've only gotten to work in online latex tools.

There are plugins to do this in Vim, Atom and I'm sure other editors as well. See one academic's description of how to tie it all together here: http://wcm1.web.rice.edu/plain-text-citations.html

I would second this, having written a lot of documentation recently (markdown + template + pandoc -> pdf) I am very interested in improving this workflow.