@adrianmc I think the appeal of CRA was that you didn't have to worry about any of that. It was all basically decided for you. If you start having a bunch of options you might as well be using Brunch straight up. Perhaps a better option would be to create a well known set of curated Brunch skeletons for various setups.
Well you could poke the project name into the package.json file :) and if you want to go down the route of customization then you may want to create an interactive experience which prompts the user for choices if they care
Do you want to use a CSS preprocessor? (If yes prompt with some options, if no, use css-brunch)
I guess you could take the task of plugin discovery and make that easier
And you either have to have a skeleton for each combination or build up the template somewhat dynamically.