If you are using the modules system on the server side, you do not need to use Babel at all. To use modules in Node.js ensure that:
- Use a version of node that supports the --experimental-modules flag
- Your *.js files must then be renamed to *.mjs
That's it.
However and this is a big however, while your shinny pure ES6 code will run in an environment like Node.js (e.g., 9.5.0) you will still have the craziness of transpilling just to test. Also bear in mind that Ecma has stated that release cycles for JavaScript are going to be faster, with newer features delivered on a more regular basis. Whilst this will be no problems for single environments like Node.js, it's a slightly different proposition for browser environments. What is clear is that testing frameworks have a lot to do in catching up. You will still need to probably transpile for testing frameworks. I'd suggest using Jest.
Also be aware of bundling frameworks. You will be running into problems there.