There are a few animation-centered applications that output to swf natively. At this point, Flash itself, is more of an application development environment than an animation tool.
By far the most advanced and full featured is
Toon Boom Studio. This is seriously a killer app for animation.
Toon Boom also makes a "lite" version called
Toon Boom Studio Express. It is still a hell of an app, but doesn't have the power of the bigger package.
Moho is another animation app that will do for some more basic stuff. It is much cheaper than the other 2 apps, though.