A common way of avoiding the long build-times is to divide your project up into multiple projects and reference them in as SWC's in a Main project.
Actually the shorter build times are mostly considered a positive side effect, as any larger project really ought to be divided into multiple project. Typically you will have more than one library project, handling the service layer/ controller ect.
This way you could for move the controller/ game logic to one project. This would have longer intervals between changes, and therefore you could close this project, building only the one you are currently working in.
If you are using a lot of assets from Flash ect. move those to a SWC as well.