In any case: "It's the authoring tools stupid". The fact that the official client is closed helps prolong the authoring empire only slightly. Even if a working and complete client becomes Free Software workable authoring will only be available to those who fork serious bucks for a long time to come. These problems remain even if flash is somehow cleared of its dependence on patented codecs.
The Web standards have caught up with most of what flash can do: SVG, Canvas, Video, Audio, fast JS engines, etc. Unfortunately, you can only use those things if you target the few aggressively standards following browsers. Thank you IE. :(