Built in npm support is huge for me. I use Scalajs full time and one of my biggest issues is having to use SBT and webjars. I also end up using some mashup of npm modules as well later on in the build which complicates it even more. Plus the speed of the compiler becomes a massive issue, especially during unit tests.
By turning it into a more readable Js, I wonder if the debugger would play more nicely too. I've noticed in Scalajs the debugger randomly misses breakpoints or moves to the wrong line sometimes. Anyway not a rant on Scalajs, I do like it but there's definitely some bottlenecks for me.