The first snippet uses the CommonJS [1] standard (a way to import packages into a JS file that is used by Node, webpack or browserify for example).
The second snippet uses ES6 modules [2]. Babel actually transpiles those ES6 modules into CommonJS modules when used in a Node.js environment (which is the case with a build tool).
Since even IO.js doesn't support ES6 modules for now and you're likely to use a build tool in order to use babel, you shouldn't use ES6 modules in a build file.
The second snippet uses ES6 modules [2]. Babel actually transpiles those ES6 modules into CommonJS modules when used in a Node.js environment (which is the case with a build tool).
Since even IO.js doesn't support ES6 modules for now and you're likely to use a build tool in order to use babel, you shouldn't use ES6 modules in a build file.
[1]: http://www.commonjs.org/ [2]: https://developer.mozilla.org/en-US/docs/Web/JavaScript/Refe...