Believe it or not, a majority of big-name sites are still using Flash, along with open-source JS players.
Exactly. Sites now have to provide the same functionality twice, because the browsers have made such a mess of standardisation that you can't rely on a single implementation to actually work portably.
It seems to me you're complaining that using new features that aren't yet standardized, aren't yet standardized. I can sympathize with your frustration, but then if you don't like it, don't use them.
Unfortunately, in the real world, that is often not an option. If your client wants multimedia elements on their site, you're going to need HTML5 multimedia elements despite the fact that numerous aspects of how they work aren't standardised. And just to be clear, this is stuff that has been available in browsers for 5+ years now. It's hardly some new development, and failure to standardise effectively after such a long period is just a demonstration of how worthless some of these standardisation processes have become.
Ultimately, what matters is whether your site works in visitors' browsers. Standards are only a means to that end, and validation in turn is only useful if you have useful standards to validate against. Since a lot of the web standards today are borderline worthless due to their instability and/or their failure to specify so many aspects that make a difference in practice, validation doesn't really give you the assurance you seek of compatibility either across today's browsers or with future browsers.
Once again, I'm not saying the world wouldn't be a better place if you did have that assurance or that I agree with the path the browser makers and standards bodies have chosen to follow. I'm just saying that as a web developer you have to play the cards you've been dealt, and I don't see formal validation as improving your chances to any useful degree today.