Here is what makes jQuery slow, both now and in the past:

* querySelectors (standard or the home grown Sizzle engine)

* Method chaining for trivial tasks, in many cases to compute data that is already statically present or directly assignable.

Regardless of whether jQuery is using modern APIs or not there are old standards available, to JavaScript, that just about everything in jQuery eventually compiles down to. At the end of the day it becomes a matter of whether writing a couple of 3 line abstractions is far too hard of work or whether it is simply easier to push everything through 65k of jQuery purely for the sake of familiarity.