As far as I know, Flash is a sloooow compiler. Its one of the reasons I work with Flex Builder. Flex's compiler is surprisingly faster! It also has several compiling modes, each useful for a particular purpose, debugging, releasing, etc.
Perhaps there is an easy trick to solve your situation, or you could even try to analyze what is causing the long compilation time. I can think of disabling swf compression for debugging, and things like that. Beyond that, what I do to ignore the problem from the root, is to take certain architectonic cares in your application building. For instance, dividing your app in compilable modules. As complicated as that may sound, the simple fact of compiling your graphics, sounds, etc assets in a different swf usually helps. Using this, assets are compiled in one place, and their "behaviour" is compiled elsewhere. If you think about it, there is now reason to recompile all the movieclips in your work, just because you changed a parameter controlling the animation in one of them. Look up on techniques to link Flash with Flex to explore deeper in this topic. Furthermore, there are more advanced ways to divide your application in modules, that is, independent parts of the application that are compiled separately but are all compatible to one main swf. This, I would say is something that comes with time, and it requieres quite a lot of design patterns knowledge. Maybe not what you were looking for, but I guess there is 5% chance that it is, so hope it helps, Li
