The difference is that Flash is produced solely by Adobe. Their rendering technology is closed source and produced by a single team of developers. No one can contribute to their performance except them. There are many browser developers working on their technologies, and Webkit is one of the largest currently. It's an open source project that any good developer can contribute to. Mozilla is the same. This means that if one browser is doing really power intensive animations, you can either switch to another or contribute to the performance of your browser by writing better animation code and submitting a patch.

We're a long way off from web ads being as animation intensive as the latest 3D games. Browser rendering technology can reach the point where the animations that we're used to seeing these days can be optimized quite well, especially if the graphics card is involved. Real strides in the power of HTML5 animation has only reached an awesome level in the past year or so. Next year things will be even better, and it will take advertisers a lot longer to move on from Flash.

As for ad blockers, they have been blocking non-flash content for years now. Google ads are HTML and javascript based, and they are blocked just fine. Same with popups: all javascript. Most advertisers are not going to spend a hell of a lot of time trying to get around ad blockers, since they work with mass distribution and an awful lot of punters don't care about downloading and using an ad blocker. The only sites that try really hard to make you see or click on an ad are usually scams anyway.