>but now much of jQuery's goodness is native

Since I never really learned jQuery, I can't attest to how much of modern JavaScript is based off of it. But looking an a quick reference for jQuery, it's pretty obvious that a huge part of it did not become standard. So all of the time invested in learning those features is wasted. Any application using those features is permanently locked in to a nearly obsolete framework. And the owners of those applications is now forced to find developers who both know and admit to knowing jQuery knowing they'll be dooming themselves to supporting old legacy code.