Wow, worrying so early! I think this is an area where Adobe will be seriously concerned. Certainly things are still in the formative stages and it's all still a bit of a wild wild west with evolving standards.
Personally I think we are all forced into a huge (and temporary) wait and see to see what eventually shakes out. My guess is that Adobe will emerge with a new version or an update that solves the issue for us.
I would encourage anyone worried about this to pause and submit a Feature Request so that Adobe has a better feel for the scope of users that are interested. (Link to Feature Request is in my sig)
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I'm not that worried. But as my work implies a lot of Capitave, my boss will surely be a little bit worried by all the money he will put in my project in the next months.
I'll do a Featured Request, thanks for the quick answer.
If you read the news carefully, it is only the mobile version that will not support Flash plug-in, not the desktop version.