For better or worse the web never did that work, HTML+CSS+JS is meant to be both a way to make static websites, but also interactive e-shops, but also mail clients, but also videogames, but also ultra-heavy single-page apps like Discord etc...
And that's the greatest power of the web, but I can't see how this state of affair won't lead, one way or the other, towards a more monolithic architecture. Keeping HTML and CSS cleanly separated and JS only for the fancy stuff (but always optional!) is noble but it's a pipe dream when the use cases are so diverse. WebAssembly, or something like it, seems to be clearly the path forward.
Overall I think we should be happy too, at least it's not a closed source blob. Remember how long it took us to get rid of bloody Flash? Actually if Steve Jobs hadn't decided to drop it from iPhones I wouldn't be surprised if it had survived in common use to this day.