I really despise FLASH as "whole site" technology platform. It's heavy, it's visually overbearing, and I have yet to encounter a pure flash design that works - both for SEO and the end-user experience.
How many times have I visited a site where the main entrance is a flash intro (without a clear way to skip it)... and get to the clean, uncluttered HTML material.
Flash is great... when properly exploited (as others have said) for multimedia demos, intros, etc. But I would never do a pure Flash site...
All my $0.02 of course.
Rob