This template comes with browserify, babelify and babel-preset-es2015. Run npm install to download the dependencies.
Add your ES6 code to src/app.js. You can build it manually by running npm run bundle or it will run automatically due to the before_prepare hook. I added the hook in the scripts directory. Either approach will bundle src/app.js into www/js/bundle.js which then gets copied into your platform specific directories on prepare.
You may need to add this into your config.xml file to get it to work. Anywhere in the root element is fine.
<hook src="node_modules/es6-phonegap/scripts/appBeforePrepare.js" type="before_prepare" />