One of the biggest advantages of flash was that beyond a few DOM wrangling capabilities it basically threw away the rest of the browser and was really more akin to a Java applet than being part of the browser.
This meant that even somebody using IE6 can have a good experience with a flash app, assuming their flash is upto date.
What annoys me with HTML5/JS apps is I constantly see people showing off demos of something cool they did with the "open" HTML5/JS tools.
Then I load their demo and it's all like "hey, sorry your not using the latest version of Chrome come back when you've installed it"
Hopefully this will get better over time , but you've still got IE dragging it's feet and doing things a bit differently + Microsoft's habit of dropping support for new versions in older OSes.
Maybe the answer is for all browsers to just standardize on one rendering engine / JS implementation otherwise I can see this becoming a nightmare and everyone having to keep multiple versions of multiple browsers installed just to run all the apps they need.