YouTube's latest blog post indicated that some changes are on the way. Google has opened up a call to submit and vote on ideas. HTML 5 open video with Free formats has dominated the vote, maintaining over twice as many votes as the next-highest item almost since the vote opened up. You may vote here (Google login required).
Really interesting to see the huge number of people who want to see Flash gone from a revamped YouTube. I'd love to see Theora personally.