Google is working on J2Cl (as mentioned already by Emilio), which is (will be) a transpiler from Java to ES6 (as understood by the Closure Compiler, hence "Cl" in the name; the Closure Compiler –or Babel or whatever– then being possibly used to transpile ES6 to ES5 or ES3, and possibly bundle and optimize all the code).
J2Cl is expected to be the new compiler in GWT 3.0.
Any ES3 or ES5 script is a valid ES6 script; all JS engines supporting ES6 do "only" support ES6, there are no "modes" to be triggered by some configuration or what not (contrary to the old E4X for instance).