And then of course, there's WebGL; even if you just use it for 2D stuff (shameless plug: http://www.phoboslab.org/xtype/ ) it's way faster than Flash. I have no doubt that in a few month the the 2D canvas context will have the exact same performance (if not better) as WebGL for 2D stuff.
http://www.next-gen.biz/news/html5-still-lagging-behind-flas...
http://iq12.com/blog/as3-benchmark/
http://workflowed.blogspot.com/2011/02/flash-player-101-for-...
http://www.streamingmedia.com/Articles/Editorial/Featured-Ar...
http://pogue.blogs.nytimes.com/2010/10/07/testing-videos-on-...
http://www.androidtabletnows.com/android-devices-news/2011/n...
http://themaninblue.com/writing/perspective/2010/03/22/
http://www.blackcj.com/blog/2010/09/17/flash-outperforms-htm...
http://www.craftymind.com/guimark3/
http://www.craftymind.com/guimark2/
But hey, let's complain about it because "Adobe is evil" or whatever! (and note: I'm an Ubuntu x64 user).
Is this what you wanted to post? This shows that the browsers' JS engines have been outrunning ActionScript for years now...
My point is that if one analyzes the data, one will find that Flash tend to win over HTML5/canvas performance more often than not. The canvas and visual performance tests are very telling.
As a side note, there's definitely a gap in code execution - that's the link you posted - but it's just one of the factors, as Adobe is well aware of that and is addressing it on the next release. The AS3 VM was much faster than JS when introduced, then they spent a lot of time not doing any optimization at all. From what I've seen from their presentations, they're ready to take that back. Time will tell.
http://pacoup.com/2011/02/03/flash-vs-html5-performance/
http://www.craftymind.com/guimark3/
The advantage of flash right now is that you can be reasonably sure that if a user has it installed, they will get a minimum set of features and performance. With HTML5, your complex app may run fine, or may not run at all, depending on the users implementation.
I've no doubt the performance gap between flash and html5 will continue to narrow. However, I'm less sure that there is anything in the design of html5 that would allow for implementations that are significantly faster than flash allows for. Perhaps someone with deeper technical knowledge of the two could comment.
HTML5 does have the advantage that it's an open platform, of course. Thus you are much more likely to actually see competing implementations of the standard.
The only way to fix it is to install a new browser, or perhaps a new version of the current browser. Installing a plugin is often easier. Rather than deal with this, developers currently just develop for and test on a few main browsers. Anyone not on these are left with no other options but to switch browsers.
Suffice to say, HTML5 doesn't really improve the situation all that much. It simply trades the closed model that Adobe uses with Flash for an open model that has been used for HTML. In either case, the only way to be really compatible is to use older well established features.
Open platforms are good, and thus HTML5 is a good development. But it's not the silver bullet that many make it out to be.
It was a fun experience, and maybe later this year I'll grab a trial of Flash and port it there, just to A/B them. But if you think HTML5 is going to replace Flash, you have a limited knowledge of what Flash can do.