IMO the JS module situation has always been terrible, and ES6 modules are the best way out we have. What made the situation complicated is not only the fight between AMD and CommonJS, but also the differences in the libraries implementations and the arbitrary use of global keywords such as "require". Picking one of these implementations wouldn't help at all, it would break backward compatibility and would result in even more confusion.
Once we have browsers native support (which should happen soon based on the recent announcements), AMD and CommonJS will no longer be needed and will probably disappear in a few years. That should be enough to convince people to bet on ES6 modules for their next project.