HTML5 has SVG and Canvas and video.
It's perfectly possible that at one point someone creative is going to create a very nice animation package that generates SVG files. There already are SVG generators there of course, but obviously they're not good enough because SVG and Flash is, so far, never mentioned in the same sentence.
But is ought to be possible. SVG does structured vector graphics, embedded scripting. The things you see done in Flash has to all be possible in SVG. Flash also has this awful notion of frames, which was a major design flaw from day one.
They should have just let you determine that you want to move an object from point A to B along a path determined by a line or curve or freehand path, and that the times of A and B can be anything and not just confined to a particular frame.
Then at playback, the faster your computer is, the better the frame rate ends up being. Slower computer, slower frame rate. As long as the object moves from A to B.
Then there are the bugs and just overall clumsy handling of Flash.
Flash can be done so much better.
So, I think that someone will at one point soon make an amazing SVG animation package that will just crush Flash.
I'm against Silverlight because it's Microsoft. Microsoft means proprietary. They do whatever they want to do. You've already mentioned different version numbers. This means your customers have to have the right version downloaded. You can count on your customers having to download major upgrades, and before you know it their entire .net install needs updating, before you can show your animations and applications.
Silverlight also doesn't work on Linux. It's supposed to, through Novell's efforts with Mono, etc, but in practice, in the field, it just does not work where you need it to.
I don't know if and how well, in practice, Silverlight works on the Mac, but I don't trust it.
Eventually, I think, that future HTML5/SVG (Canvas maybe?) is the way to go. It'll even do 3D using OpenGL accelerated graphics... (but I don't know if that's portable enough).
In the meantime, Flash is your safe bet, and it's almost guaranteed to run anywhere.
I wonder if anyone has created an animation package that outputs to swf files that's better than the Flash IDE. Shouldn't be too hard, given Flash IDE's clumsiness.