Yeah, it doesn't serve the site well to include the animation and XHR stuff right at the top.
But if you had a small site that just needed to perform a few DOM manipulations, this would be highly relevant. If I just need to pop a div open and closed when a button is clicked, I sure won't bring in jquery just for that.
The reason I used jQuery is to have script working on every browser in the wild. Now that jQuery dropped support for old browsers, this advantage is no more (sure, I could use old jQuery, actually I'm doing exactly it, but I don't like to use outdated versions). I think that it was one of strongest point of jQuery and the that they decided to get rid of it is questionable decision.
It sounds like someone (motivated enough) should fork jQuery before the old browsers support got removed and maintain it as jQuery-legacy, backporting fixes from "new" jQuery" if applicable.
But if you had a small site that just needed to perform a few DOM manipulations, this would be highly relevant. If I just need to pop a div open and closed when a button is clicked, I sure won't bring in jquery just for that.