I agree that it can be difficult to modify functionality in the framework classes. I think that much can be done to enhance this process, and perhaps we can help Adobe out with ideas. I have found that many things can be modified by thinking differently. Some of the design patterns that the Flex team used are new to many of us developers. It's going to take time, hair-loss and some patience to get things to do what you want.
... aside from this, what really burns me up is the classes declared as final, and I know some are with good reason. Example, I was looking into extending URLRequest to support PUT and DELETE methods to support our REST based Web Services. But also URLRequest is a final class and cannot be extended. Anyway, I love flex.