This point needs to be emphasized more. All these articles just deal with video and then come to the conclusion that HTML5 is better than Flash because the video playback is smoother. What no one seems to mention is the much more complex applications that are built in Flash.

There is basically no existing tooling to build complex things in HTML5. A designer I know is working on a massive graphical timeline. It has tons of different layers and all sorts of user interaction points. It's a pretty big undertaking with the tooling that Adobe provides for working with Flash. It would take an order of magnitude more effort to do the same project with HTML5 and there would probably need to be someone involved with significant programming knowledge.

Someday maybe the tooling will exist but at the moment HTML5 just isn't a reasonable replacement for everything that Flash can do.