If you are a Creative Cloud subscriber, be sure to make note of the update to Flash Professional today. Despite being listed as a "Bug Fixes" update, this is actually a quite significant update as it now includes the ability to natively create HTML5 Canvas animations. This is done via the CreateJS library.

After updating Flash Pro, you will see the option right away in the opening dialog:

As a test, I wrote a quick and simple animation and then published it. The result - as expected - wasn't a SWF but HTML and JavaScript. You can see an example of the output here: http://www.raymondcamden.com/demos/2013/dec/3/Untitled-3.html. And of course, being HTML5 based, it works just fine in iOS:

For more information, check out the documentation and let me know what you think.