try some of these
http://sixrevisions.com/javascript/10-impressive-javascript-animation-frameworks/
http://hacks.mozilla.org/2009/06/rendering-svg-canvas-burst/
http://raphaeljs.com/
I've been thinking of the same thing, going with javascript rather than flash on some stuff. This works great for small components inside a html website. But to do a whole js site, I'd strongly recommend AGAINST that.
From my experience, the same animation in flash vs javascript... JS is more processor intensive. I don't want to comment on as to which magnitude, but it's noticeable.
Bats also have a funny way of dealing with javascript and ajax content, so don't expect the same result in terms of SEO just because you're not using flash. But because people have used javascript to do content injection/replacement crawlers might be better at searching through the info. There are other ways of dealing with Flash SEO issues. (Gaia framework is not a bad starting point)
Another advantage of not using Flash or Silverlight is that most mobile devices ignore this stuff. However if you're planing on creating a site that acts like flash, the usability across these devices will likely not be consistent.
If you do decide to go this route, it's going to be much like going into a jungle and hacking your way through. Whereas with flash you're likely to be going through a well marked and paved landscape. You can get to the end result either way, but consider how much effort it will take. Flash has internal and community libraries that do all kinds of stuff, with js you'll be writing a lot of your own code and will have beta libraries that might not work well across all browsers.
But on the upside, you'll be a pioneer :)