I don't really know anything about swf or flash, but I remembered seeing the
Flash for Linux project mentioned on Slashdot. It is aiming to be a Flash clone, and you can already animate 2D objects using timelines.
I'm not sure, but I think the
World Wide Web Consotrium have a standard for animation in Structured Vector Graphics, which would be the obvious choice, rather than re-inventing the wheel as with the codecs you mention.
As linux gets more attention, I'm sure projects will be started to develop apps to do most anything you could want a computer to do. I just wish there were more OS games.