Adobe showed off a prototype Flash-to-HTML5 converter last October, and now it's released an experimental Labs version for all to try. The tool, called Wallaby will enable developers to convert their Flash code in HTML5, which will get around that nasty "no Flash on iOS" issue.
Released at Adobe Labs, not all Flash features are supported, but you would expect that, particularly with a tool that's not even called beta, but experiments. The Wallaby release notes outline the known issues.
The initial release of Wallaby doesn’t support the conversion of ActionScript, movies or audio, so it is hardly a solution, but it's a start. Adobe will work on implementing these features and perhaps someday we'll see an easy conversion process for iOS (which is really, the target).