The only thing you (likely) cant achieve with plain old html + javascript there is if the Flash is actually editing the audio itself (and is not just getting a server to do it).

I don't think thats a very common requirement: there are other, much more straight forward barriers to replacing flash with html + js, such as lack of dev/designer skills (ie. number of people whom can do that in flash vs whom can do it in html + js).

Absolutely, Audiotool is amazing. I really like what they did with the nissan site, but you can still see that it doesn't flow as smooth as flash.

ambitious but not impossible