I am not a js dev, but isn't the issue of no-framework that you have to write a bunch of code to deal for various browsers? And a bunch of more code to deal with basic web patterns that you'll end up copying from project to project?
For me, jQuery is the bare minimum requirement. I would never attempt to write a large app in pure JS, even with babel. You would definitely run into some of the problems you mentioned.
EDIT: I see now where he mentioned no-framework JS
jQuery helps here
The advantages of native are that it's extremely snappy to use and fast to load. Bears smaller memory footprint (have to use angular.js at work and god it's awful) and with newer things like async await, ES16 classes, etc code management is very good. Can't recall the last time I had to take care of a specific browser quirk.
No, because it's 2017, not 2007.