Even if your target platform didn't have ES6 modules, Babel is probably not the tool you'd want to transpile those with. Let the bundler (which is the topic of the discussion here so I assume a bundler is used) handle them. Tree shaking works better that way anyway.
Also if JSX or similar JS extensions are the only thing you need tramspiling for, you might want to look at Sucrase [1] as a fast alternative to Babel.
