I hope our messaging is clear on this, but there is absolutely nothing wrong with using jQuery!!!. There are a number of scenarios where jQuery makes general web application development much better, and it is completely worth the various tradeoffs.
The thing that we (as a community) have been working so hard to do is completely decouple Ember itself from jQuery. It may not be obvious, but Ember from well before 1.0.0 all the way through 3.1 or 3.2 (sorry can’t recall exactly ) fundamentally required jQuery to be present or it wouldn’t work at all. THAT is what we have been working to fix.
Sure, soon enough Ember apps will be generated without jQuery, but Ember apps ship without loads of other really great software that you might eventually want to bring into your app to make your application easier to write (e.g.
moment, a zillion awesome addons, etc). JQuery is in good company here.