I'd be inclined to argue that the biggest problem with Flash sites is that they can add needless complication and download weight without actually improving efficiency. However, for sites which are heavy on Flash (games and video being the obvious offenders), there's always been a bigger problem: content in Flash rarely if ever gets picked up by search engine indexes, rendering it near-invisible to casual visitors.
That problem may recede with news that Google is now automatically indexing all text labels within Flash files, meaning that those elements will now show up in relevant searches. (Yahoo! is also planning similar changes but hasn't made them live yet). No special changes are required to have Flash content indexed, though it may be a few days before any relevant material shows up in searches. If you have Flash material you don't want indexed, Google recommends incorporating those purely as graphic elements, as it only indexes specifically marked text (so no video subtitles, we assume). In any event, don't be surprised to see more Flash material show up when you search Google, and a possible new round of SEO wars as sites fight to top the rankings.
Flash now indexed by Google
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