Angular CLI uses Webpack with ts-loader under the hood, and it won't use babel to transpile js files out of the box.
If you have a large app you're turning into a hybrid and it's all written in JavaScript not TypeScript and you need to transpile ES6 code to ES5 (e.g. for IE11) you have two options:
This will mean your ts files will be transpiled into ES5 and it should be all sweet. But if you have a lot of js files this can take a long time.
As of CLI v6 you can now customise the underlying webpack config! 🎉
Use one of the following tools to customise your webpack config and add babel-loader to transpike your js files into ES5: