Right now you can use Flash to work around a lot of JavaScript limitations and many products use an invisible Flash movie to for example batch upload files (Flickr, Wordpress), play movies in a screenreader accessible manner (with DHTML controls outside the main movie - Yahoo Video, for example) or automatically add content to the browser clipboard (snipurl.com).
All of these will cease to work without user interaction in flash as reported on the adobe devnet. There are very good reasons for it as explained by Lee Brimelow but it is a real problem that will cease to make Flash a useful tool to patch inaccessible solutions.
As long as you cannot access a Flash movie in non-Internet Explorer browsers via keyboard, there will be no such thing as an accessible flash page. Research findings presented at Scripting Enabled last week showed that for example many screen reader users skip Flash as soon as they hear that there is a movie on the page, regardless of how much effort you put in to make the movie itself keyboard enabled. DHTML controls worked around that issue - a button that cannot be accessed is very secure, but also pointless.
There must be some middle ground there somewhere
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