Don't use babel-preset-es2015 (or maybe drop babel completely?)
Use babel-preset-es2015-node4 instead of babel-preset-es2015
Since this generator's package.json specifies required nodejs version as 4.2.6, there's no need to use babel-preset-es2015. ES2015 babel preset makes babel transpile all the codebase from ES2015 into ES5 even though node.js 4 can understand parts of ES2015 syntax. Therefore babel-preset-es2015-node4 could be used instead to make the development process even faster.
Alternative: Require nodejs 6 and drop babel completely
Nodejs v6 supports over 92% of ES2015 (according to node.green). If you agree to require nodejs v6 then there's no need to have babel as a dependency anymore. Nodejs v6 becomes active Long Time Support version in October 2016.
Well the main target of the generator are Web browsers. I'm not sure we can already forget about ES5 (?)
Yes, but as far as I understand the codebase, Babel is not used for client-side code. It's only used to transpile gulpfile, isn't it?
I get your point, you're right as far as the build of the generator itself is concerned; the same is true for the build of the modern-web-dev-build project :)