There's still stuff you can't fully do with JS on all browsers with market shares large enough to cater to. The problem with Flash IMO was more how people used it than the technology itself; if we wanted to make sites with large photo backgrounds that blur and have some slight movement of elements, that was pretty easy to do with Flash 10 years before it became easy to do with JS. The vector stuff was huge at the time.
Lastly, re: CPU usage (mentioned in article), Flash could be a hog, but plenty of sites still eat 100% of 1 core just to re-sort a list of things on screen on a maxed-out rMBP because of their poorly-implemented logic in whatever the new JS framework is this week. Flash at least wasn't usually that bad, and graphics smoothness was way higher with Flash than stuff I've seen using JS animations.