I agree in the main that DOM manipulation is the root of all JS sin, but the list you provide is not my experience as all. Like all code, well-written JS+jQuery ought to be self-documenting. Again: caveat is well-written. The learning curve is no steeper than figuring out JS's own native esotericisms. Yes, jQuery is slow as fuck. $('#something') is something like thirty times slower than document.getElementByID(), BUT when you are in the realm of milliseconds I will trade those extra keystrokes because I'm on a deadline, and the user will not notice 99 times out of a hundred. Almost every time I've had to diagnose slow jQuery, the author was doing something bad, like reselecting the same DOM elements in tight loops.
IOW, there has to be a balance between performance and ease of development, and jQuery is my optimal point. Sometimes it's the wrong fit: when speed is the overriding factor above all others, it's not appropriate. But to extrapolate that into a never, never, never rule smacks me as throwing the baby out with the bath water. The problems with it are usually academic, not practical.