Some transitions make a lot sense when they are created with MovieClips. You have a lot of individual objects moving around on the screen. Moving MovieClips around is what Flash is all about.
But other types of transitions really work against this. Imagine a transition where the image of the stage is cut up into strips or squares. In this case the transition might cut or divide the stage into blocks that are not separate MovieClips. Imagine transitions based on pixels rather than MovieClips.
Here’s an idea, before showing content create a Bitmapdata object of the content. Manipulate this to create a transition. When the transition is complete, replace the BitmapData with MovieClip.
The key here is that all of the content is stored in a MovieClip. This way you can easily place everything on the stage in one move. You can also easily create a BitmapData Object of the content using the BitmapData.draw() method.
Here’s a couple examples that show off the idea. http://webdevils.googlecode.com/files/BitmapTransition.zip