They ended up having to add classes (albeit as syntactic sugar).
Argue its advantages all you want, but I'd say that's representative of what a failure it's been. One of the last languages supporting prototype-based inheritance has basically given up on it.
Personally, I find it an awkward way to try and encapsulate code, generally, it has terrible performance to boot.
Was there ever any issues with prototype-based inheritance? I've always assumed that they added classes simply because of stubborn classical-based programmers who couldn't bother to learn JavaScript correctly.