I used to get really excited about Flash websites but these days all I see are the cons that Flash can bring to the user experience:

A.) I feel like I’m being dragged through the experience, waiting for the site to load, watching the pre-loader etc.

B.) Waiting for things to move around is irritating when all I really want is the content. 

C.) As a developer, it is tedious to keep flash sites up to date, also tedious to build an XML framework for content management.

D.) The best flash sites are ones that move really fast, the motion interferes minimally with the navigation, which makes me wonder why the motion is there in the first place.

Caveat: When Flash is not the means to an end but rather the end in itself, it can be beautiful and not annoying at all.