I don't think this point stands, or at least it doesn't in the way you think it does.
Flash has two text rendering modes: native, and embedded. Native uses the system API and follows your system options, like when deciding on how to antialias. Embedded uses the embedded fonts with the antialiasing method the developer chooses. Many developers pick the latter because they want to know exactly how text will work on all platforms.
It's up to the developer to select which method to use. And the new flash.text.engine.* API make both a lot more powerful.
> Second, copy-paste, as others have pointed out, is a problem (...) enough apps out there fail to enable it properly
Like the first one, this becomes a developer choice, not a platform problem. It's not that "it can be done", it's that it's easy. People who don't do it, don't do it because it's the option they've picked, not because it's difficult or anything.
Your third point totally stands as having a separate DOM kills the user's control over the content and its form. But point 1 and 2 are due to conscious developer decisions and not the technology.
Funny that on hacker news this gets to the top 10 news items and people even comment on it. On proggit anything related to Aviary is downmodded to hell and beyond... simply because it's about Flash.
I'm not sure where's the advantage.