Actually, the GPL makes total sense for end-user software. In fact, lots of people argue that it makes the most sense for downstream software since it protects user freedom and won't be used in a way where compatibility is an issue. But you're right it makes sense for the OS too. I guess the GPL just makes sense, period.
Maybe it's just a matter of a complex system, vs something more simple... a JS module can be used much more broadly as MIT/BSD/ISC than with GPL... and for the most part, because JS is typically open (though obfuscated as an artifact of minification)... where something like a complete application, or OS would have a greater desire for those safeguards... A client library to an application, less so.
