I'd still say the major misuse I've seen with Flash, especially amongst non-English (in my case Taiwanese) sites, is that it adds absolutely nothing to the user experience. It just looks “cool”. But I guess the crawlability of the Flash on those sites won't help them much anyway.

It is best practices for usability and accessibility to provide textual elements for non-visual or non flash users. In fact it would also open up a site owner to potential lawsuits if they didn't since disability laws require it.

For those reasons I would be very surprised if Google imposed a penalty for supplying a text version of flash websites. I haven't seen any official word or research on this though so I could be wrong.