Recently, I started a brand new React project, router v4 was near release, and a few other bits that were new (to me), using Webpack 2 for the first time, and a few other bits... to be honest, it was about as frustrating an experience as I've had in bootstrapping a new project. Now, it's not as frustrating, but it's really the first time I felt *that* frustrated, so I can feel the pain of a lot of others.
That said, I would never want to go back to the old days of manually bundling, or using script runners for bundle/reduce... Or doing manual namespacing in JS to avoid collisions in a large project. Modern ES6 (or node/cjs) modules are much cleaner, and you can take my Babel before browsers support all the current stage-2+ features I use from my cold dead fingers. It'll bee 3-4 years before that really happens. And it will be weird the transition from build/deploy bundling to JS modules from the browser, and HTTP2 server-push. I still prefer the way JS is written today vs any time before.
I use a lot of async functions, and some ES6 classes (sparingly) where needed. There are a lot of great things in writing modern JS. The flip side is evaluating modules in npm, and keeping up with some of the proliferation without falling into the trap before they're ready, or likely to take established roots.