EcmaScript 6 and 7 are actually adding beautiful language features. JavaScript is changing in a big way, a lot of new JavaScript will not even resemble the stuff you're probably referring to.
If you are saying this, you certainly didn't read the article (properly).
You can not "eradicate old legacy libraries" on whim - this stuff is out there. It is used by software out there. Software that would break if things like that would be removed. You can't just rip out and change parts of it at whim. You have to work around problems - at least until they wane in popularity and slowly die out. Evolution, rather then revolution - as stated in the article. That is exactly what TC39 is doing when they are improving on the standard and JavaScript itself.
Case in point: Array.prototype.values was a proposed feature - returning an iterator for the values in an array[1]. The feature was introduced and had to be backed out at least twice[2] because widely used web frameworks (in this case, Sencha) used the attribute "values" on arrays and webapps broke as the method was added to the Array prototype. And this wasn't the first case.
So, that's the thing, right, despite all the downvotes above.
We get to strongly push for new language features, or we get to strongly push for backwards compatibility.
If we elect to do both blindly and without forethought, as the JS community seems to be doing (having learned from the C++, evidently), we are going to run into these things over and over again.
And frankly, a lot of the legacy code and terrible hacks on the Web deserve to be broken, noticed, and remove/updated. Hacking prototypes (as Sencha did here) is something they shouldn't have done in the first place.
The origins of this code come a bit before jQuery.. when libraries commonly extended existing structure prototypes... Some of those became the basis for the additional methods (map/reduce/filter etc) on Array, and others. JavaScript is very flexible which is a blessing and a curse.
I've been a fan of JS since pretty early on... the DOM differences between IE and NN were really horrible to deal with in the v4 browser days, and until jQuery didn't start to get much better really, where today you really don't need jQuery. It's an evolution here... If you're willing to use transpilers you can go anywhere you like... from BabelJS to ClosureScript, TypeScript, CoffeeScript or others... you can get the style you like.
npm + browserify (or webpack) have made developing modern web applications a dream compared to the past.