Of course, these could eventually be fixed, but I think Adobe's smart enough to make sure that Flash doesn't stand still.
Flash has the same problem as IE -- nobody upgrades it, so you can't use new features unless you have something very cool to offer. (YouTube may convince people to upgrade Flash, but your advertisement sure isn't going to.)
Anyway, Flash's big advantage is its IDE. A non-programmer can produce simple animations... and I don't think that's possible yet with Processing + JS.
The performance issue is not too worrying -- the new JavaScript VMs should make this problem go away.
It would also be possible for browsers to support most video formats natively, and allow JavaScript to control the playback.