There is a trade off being made. The whole point of the presets system is to not bring in the modules you don't need. As the Node.js runtime and browser ES6/7 feature support grows, you will not need certain plugins.
Your title is a little inflammatory: "a lesson in how NOT to design software.".
Re: Javascript tooling. Yes is it painful. But Babel is designed exactly as it should be, and the solution to fix your problem is a library that wraps around it.
He did suggest how to fix it—enable everything by default. If you'd like to argue against that then that's fine, but your response makes it look like you didn't even read the article.
Your title is a little inflammatory: "a lesson in how NOT to design software.".
Re: Javascript tooling. Yes is it painful. But Babel is designed exactly as it should be, and the solution to fix your problem is a library that wraps around it.