1) Video.
Video on the web is king. Streaming video. Live video. Video comments. Video video video. None of these javascript-based solutions have an inherent solution for incorporating video into your web app, and therefore will always need to be augmented with a video technology for web-apps that require video.
2) Cross-browser compatibility
We're getting closer with javascript compatibility, but not there yet. Yes, many of these frameworks claim to hide the issue, but what about developers that want to develop components for the framework? A virtual machine that is consistent across all browsers (well, supported browsers) makes development much cleaner.
3) Flash IS Open-source.
Flash may not be truly 'open-source', but rarely is there a mention that Adobe has released the specifications for the specifications for both the .swf file format and the actionscript virtual machine, and are accepting feedback on both.
4) Rapid Development Environments
I admit to knowing little about how people are developing these apps in these languages, but doubt that the IDE's contain the feature-rich capabilities required for complex RIAs - things like code hinting across libraries, a walk-through debugger, visual drag & drop component interface, etc etc.
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I am in no way suggesting that these new technologies are not exciting or an improvement - I just think the hype around them (http://www.roughlydrafted.com/2008/06/14/cocoa-for-windows-f...) is somewhat unsubstantiated. They still have a long way to go. But it's great to see some new competition creeping in on the big guys - good for the consumer!