Maybe a writing up a road map first for this would be awesome - defining what features would be core to scaffolding a project, and what would be opinionated and project specific.
I am coming from a front-end perfective, and getting a configuration set up for asset pipe line, css preprocessing, image optimisation, and authoring & linting is as important as is it repetitive.
I am currently in a PR that will introduce stylus/less/sass(sass-node) support, but it got me thinking: should these options be a part of the mern init. Like, mern --css stylus - which would also introduce a .stylintrc and stylint-loader.