Whole flash sites are not smart. If not for size and support reasons, as Twey said, their content cannot be indexed by google and also, screen readers for the blind cannot read flash content.
Now, one of the few uses of flash is for music players. For several reasons, flash works great for this. But flash, like everything else, can be useful in the right context. As Twey said, if you're running a game site, make the games in flash. If you're MySpace, make the music players in flash. If you want to display your artwork, go with an AJAX scroller, not a huge flash file.
And that's my two cents.
Thou com'st in such a questionable shape
Hamlet, Act 1, Scene 4