This is something we looked at for a while when starting out, and even posted on HN to ask about (http://news.ycombinator.com/item?id=203864). In the end, we chose Flex because it seemed like we could get good enough performance while enjoying the benefits of quicker development. We mostly use pure AS3, but we saved some time with a few components. Hopefully someday we can strip those out and cut the Flex framework overhead.

But yes, Flash player has an unpredictably crappy internal clock and performance varies significantly based on the browser and OS, so synchronizing the notes with the music has been a challenge. For the most part, I think we've done a fairly good job compared to the existing players. We scale intense tasks dynamically in game but there is definitely room to improve (custom a/v delay, controller delay, really-crappy-performance mode, etc).