Raphael also suffers when animating many elements, here is a question I answered about a week ago on StackOverflow and I ended up solving with d3.js:

http://stackoverflow.com/questions/8239235/smoothly-animate-...

But recently I went through Raphael's source an I saw an implementation on requestAnimationFrame, perhaps Mike can shed some light on what is different. Great work on d3.js by the way!