I have the feeling that Flash-based ( or Silverlight-based) websites are generally frowned upon, except when you are creating games or multimedia-content rich applications.
I am a Flash developer.. and I have found that although Flash requires more effort in coding, the potential is enormous. You can create very simple sites with simple transitions, so subtle it would seem to be a normal HTML page, while still being just as light.
At the same time, you can use OOP with ActionScript to create a website that is as complex and as inclusive, as well as feels and acts like a desktop application. WHILE ALSO REMAINING VERY LIGHT! (only the content required is loaded on demand, as apposed to 4 column HTML sites with far too much information.)
Nowadays, and this is still without migrating to ActionScript 3, but still using ActionScript 2, MY flash files contain simply 2 or 3 lines of ActionScript, only one frame, and an empty stage. Everything else is dynamically created or added at runtime.
Flash's problems are not about Flash, but about lazy development.