If you read carefully the old Gruntfile.js, you'll notice it was already using a watcher, only recompiling changed files (cf. newer task), and loading babel only once. (I did manage to get a similar setting with gulp and watchify but it was significantly messier — my experience is that gulp is verbose more than it is flexible...)
And yet, getting rid of that transpilation step, be it 5s from scratch (+ maybe several minutes or more of npm install) that has to be run on every CI run, or ~1s of recompilation, that I still have to worry about when developing, is freeing. More than once, I've gotten bit by relaunching the app before transpilation was over, or relaunching it while transpilation had failed with an error and it was buried in a console somewhere.
I appreciate the help trying to make Babel work for us, but I'm not trying to make it work for us anymore, it's simply come to a point where both Node.js and Chrome support most of the features we were using Babel for anyway (except for async/await, which nodent does better than babel anyway), and getting rid of transpilation is simply a mark of the language maturing. We couldn't have done it even a few months ago, so really, it's all good news :)